digman

If all else fails, this is what I do...
EDIT: forgot to add be in Ortho mode...
Turn on the 2D grid with snapping on.
Zoom the model in really close
Line the grid up on the center line of the model, yes you are eyeballing it... remember this is if all else fails. You can get really close and in most cases it is good enough.
Now, use the pick in the symmetry panel,(leave global space selected in the panel) hover the cursor over the line that is on the center line of the model.It will snap to that grid line. Now left click the mouse button.
Now the symmetry is very close to being correct.
Close the grid
Last but not least, just touch a brush on one side of the model... I just one click with my smooth tool set to zero... That way for sure I know one side is copied to the other in this case. Now under the Geometry menu choose "Symm Copy" 
You know for sure now that your model is in perfect symmetry... If you eyeballed it good, you should see no movement on one side or just a tiny twitch...
 
It is a last resort but works... one last check switch to the retopo room and make sure the symmetry is correct there too after doing the above...

Ok, I did one test: This time going from Blender to 3DC first and back again to Blender.
 
I opened Blender, used the default sphere.
3DC was already open.
Transferred  it to 3DC through the applink... which opens the import dialog panel in 3DC, made my choice of map resolution. etc etc
Next did some painting on the sphere
Now, under the File menu, chose "Open in Original Application"
In Blender... clicked on the Update tab
Model in Blender was updated correctly... 
Again, these are simple test, deep testing not done...

Windows Beta version. 4.5.21
When using a PBR smart material you need a curvature map for the material to be applied properly plus sometimes a AO map.
If you choose a smart material and their is no curvature map, then 3DC will automatically create one. If one is there but not calculated for your model then you would need to re-calculate the curvature map...
Textures Menu / Calculate Curvature. (second to last one in the list of choices under the texture menu.
Also some smart materials need a AO map... 3DC will tell you if you need it for that material plus giving you the option for creating one. 
I leave my creating of the AO map after baking from the retopo room to the paint room. Not everytime but a lot. You have more controls at your fingertips. It too is under the textures windows
 
 

 

I understood right way from your first post but the gif helps... I had to do some test.
 
The brush radius size always effects depth unless you lock it.  The larger you increase the brush radius from it's original depth selection the higher the depth will be, the smaller the radius the less depth there will be.
 
Now how does this work with the depth selection when using the Sampler tool.
 
First: Use the V key and do not select the Eyedropper icon (Sampler tool)... if you use the Eyedropper icon when you switch back to your brush, you lose your depth selection. Yes this part needs to be fixed, it should transfer over to your paint brush regardless of radius when switching back but I think that would take some deeper coding...
 
EXAMPLE:
 
Say you painted an area to a certain depth but now need the same depth in that area but the brush radius needs to be smaller to finish painting in that area. You use the depth picker in the Sampler tool to select the depth and of course since the brush radius is smaller it has to increase the depth amount to match the depth your are picking (remember what I talked about at the beginning of the post about brush radius and depth). 
 
You can do the same thing by picking a certain brush radius and depth value and then locking the depth... As your brush radius gets smaller or larger the depth value changes according. This takes careful planning though to remember your settings if having to work more in the same area later.
 
This appears to more of a feature than a bug I would say. Imagine painting on a model then needing to fill in some areas later, it would be quess work on figuring out the exact brush radius and depth to match that area.
 
Also as side note, select or deselect "additive painting" under the depth icon according to your need.
 
If you have some suggestions for the tool, then by all means put in a feature request...

Try the Texture Baking Tool under the Textures menu in the Paint room.
 
Have the bad polygon model you textured in the paint room.
Now use the Texture Baking Tool
In the input section "Mesh to Bake to" navigate to your fixed model (with the uv set) and select it. Do not check "use current low-poly mesh only"
 
The rest of the input and output sections are fairly straight forward... 
 
A few things missing in the tool is that you cannot put the roughness map in the alpha channel of metalness map. I think you can use Photoshop to do that if you are using the metalness workflow in Unity. I could be wrong on that, I have not tried it myself.
 
Andrew has not visited this tool in quite awhile and the outputs need to updated for the PBR workflow.
 
The might not work perfectly and could require some clean up. You will just have to test. Please post back here your results, that will help others in future.

Here is a link to the Playlist of many available retopo tutorials.  
 
https://www.youtube.com/playlist?list=PLF62F3C31216D2794
 
Watch the last five tutorials in this series, it deals with retopoing and baking The whole series is good though as you will learn a lot about the sculpting room. I know you do not need the normal map baking part.
 
https://www.youtube.com/playlist?list=PLlQ3JITh9bXOvoKQdlX5xFJDZBhX2LRrf
 
 
A link to AbnRanger's recent 3DC's YouTube Navigation tutorial.
 

 
I think I got my way down now for the future on getting users to the tutorial videos quickly..

It is designed for a function and recommended use... Every piece of software does this, designing for a function. These models are placed inside of the 3DC folder system.
 
Once you have a scene open, use the import tool to bring in higher polygon models you created or Drag a model file into the viewport or right click on the layers panel choose import or choose to import a 3DC file.
 
 What you seem to desire is a model browser(with model icons) for higher polygon models to be placed in the scene. That would not be a bad idea so we could simply drag and drop from the model browser. The import panels would pop up like they do now if we simply drag a model into the viewport of 3DC.  That really would be nice.
 
and again if you have not gone here yet, AbnRanger has made many good tutorials on the functions of 3DC...
https://www.youtube.com/user/PILGWAY3DCoat

Yes it is the shading... 3DC has it's own way of doing things like any program.
 
The below is importing using surface mode as you have done.
 
Look at the picture and the top word is a low polygon mesh imported as is. The result is the same as yours.
 
Next word has flat subdivision applied from the 3DC import dialog box. Shading issue gone but staircasing effect because no smoothing is done on the polygons... This is great for some hard surface models but not for text. You might have enough polygons to use flat subdivision but I can not tell from the images if you can or not to avoid staricasing.
 
Next word is a high polygon mesh imported, form is good. This would be also good for voxels...
 
Last word is a low polygon mesh imported with hard edges and the normal subdivision is used from 3DC's import panel. 3DC recognizes hard edges upon import for both surface mode and voxel mode.  I personally use Wings3D for creating hard edges though any program that creates hard edges you should be able to use.
 
Hope the above helps some in understanding how 3DC works.

Under the E-Panel...  (Brush and splines Panel) deselect "ignore back faces"

Two other ways...
1.Switch to the PicMat_Clay shader. Painting density will not be pure black on the model. Then before baking to the paint room switch back to the PBR Shader.
 
2.Go to the retopo room first and place your strokes before auto retopoing. 3DC will keep the strokes and not delete them. Then go back to the sculpt room and run the auto retopo routine.

The PBR beta version and 4.1.17D need their own separate 3DC folders. In Ubuntu they are located under "Home".
I am not not talking about the folders that are created when unzipping the tar.gz file but the folder that 3DC creates when you first run it.
It appears that you overwrote 4.1.17D with the beta version under the Home 3DC folder. Some shaders were removed in the newest beta. Now when loading 4.1.17D it can not find the shaders to compile.. 
 
When you run one version the other 3DC folder under home needs a different name temporary. Then when you want to run say, the beta version you would then rename 4.1.17D 3DC folder under home to a different name and rename the beta version folder to the regular name of the 3DC folder under home.
 
I only used Home as an example for Ubuntu, different Linux distros might call home something else... 
 
The above is only a quess as you did not explain your process of running both the beta and 4.1.17D... 
 
Correct Install Process for Linux to run both 4.1.17D and the beta.
 
First remove the corrupted 3DC folder under "home" 
Unzip 4.1.17D and name the folder to something that tells you it is the 4.1.17D
Run 3DC for the first time. Re-register 3DC.
Now rename the 4.1.17D 3DC folder under home to a temporary name.
 
Unzip the beta and  name the folder to something that tells you it is the Beta
Run 3DC for the first time. Re-register if necessary.
 
Now when you want to run 4.1.17D, you must re-name the beta folder under home to a different temporary name and re-name 4.1.17D  version folder back to the regluar 3DC folder name under home. Reverse the process when wanting to run the beta version.
 
Sorry this is the way it has to work for now... PBR 3DC beta and 4.1.17D plus older versions are not compatible

26.01.2014 4.5 BETA9
- Longstanding problem with crashes in UV room/automapping solved.
 
My note: It also appeared to effect manual retopo in some cases.
 
This bug was solved in the above beta...
 
UV mapping corrected, v-direction flipped. In another beta Andrew fixed this as well.
 
You can dowload and run the newest PBR Beta 4.5.Beta15 in trial mode. 3DC Beta now has Physically Based Rendering of materials and HDR Lighting...
If you decide to run the beta, you must follow the install instructions to the letter. Scroll down till you see the red letters.
http://3d-coat.com/forum/index.php?showtopic=17076&page=1
 
I go into more detail in this thread. Scroll to the bottom and my last posting is there.
http://3d-coat.com/forum/index.php?showtopic=17467&page=2
 
Andrew puts all corrected problems in the betas... 4.1.17D will not receive the fix.
If for any reason the file still crashes at times when using the beta, then under the Help menu in 3DC, you can send the problem file to support.

The old materials tab is gone in the PBR beta and I would think it will not be in 4.5 Final...  
I created a Folder call Legacy, In the PBR editor, I then choose From Camera when creating a new material. This will make a square image and not the shader ball.
Now I have more or less the old style materials back for easy access.
Excuse the quality of the material in the pic, it was only a test... not the final material.
Also, you can use the top panel outside the PBR editor to change it to cube mapping if you like or the other projections...

Your are correct... They can not be applied to imported models.Those shaders are only available for voxels or surface mode objects in the sculpt room.
They can be baked to the paint room using a retopo mesh and the baking tools in the retopo room.

3DC does not support the uv shell format which is really what I would think you need for the lightmap workflow... 3DC simply moves the polygon faces and the uv seam layout to a different uv set. This is mainly so you can get more texture space per parts of the model.
3DC at this time does not support natively the uv shell format like Maya or other software.  A feature request has been put in but Andrew saids it requires a lot of deep recoding of 3DC. I would not expect it anytime soon.
 
The above is the best to my knowledge and of course can be corrected...

You have to deselect " Brush along Curve" first before pressing the enter key... I do not know why this is the case but that is how it works for now...

Ok, What you are describing sounds likes you need to bake lightmaps where the Diffuse, Spec and Normal map/bumps plus lighting information are baked into one uv map/image. The same you would do for a game engine. Render to Texture is the word for it in 3DMax. Lightmaps is the more general common word to use.
No need to spend money. Blender can bake lightmaps...
 
Now I just did this quick bake in Blender of a model please to not judge the quality.
I imported the model into 3DC after baking in Blender and applied only the baked diffuse map to the model.
The model you see in the 3DC viewport has no lighting information on it from the 3DC lights or Hdr. I switched to flat shade (view menu) where no lighting information is calculated.
No normal map information from using a normal map in 3DC.
 
All the information Diffuse and Normal map plus Blender scene lights are in one uv map image including the shadow on the right side of the model from my Blender light.
I used no spec in this example.
 
The flat uv map is shown in the texture editor, right side of image. The two darker spots are the baked shadows inside the cylinder and the other lighter one is the shadow side of the model all baked into the image plus again the normal map information as well.
 
The Workflow.
Create your maps in 3DC as normal.
Export the model and textures.
Import into Blender.
Set up your lights according to how you want the light and shadows to fall on the model.
Use the Baking tool for selecting the combined render pass. I use Cycles for Baking because it will use my GPU
Bake then save that image and you are done...
The above is the workflow not a tutorial.
 
I hope this is what you are looking for...
 
I will be back with a better example but thought I throw this out if you stopped by...

You will need to buy the extra licence but it does not cost much. 40 dollars... You would then download the Mac or Linux version plus you will recieve a serial number for the Mac or Linux version.
 
If you brought the Windows,Mac and Linux versions for 419 dollars, this step is not necessary.
 
http://3d-coat.com/buy-now/ 
I have both Windows and Linux versions of 3DC.

When you un-installed 3DC did you manually remove the 3DC folder under Documents/settings... I do not know where windows 8 puts the 3DC folder... I at this time no longer use Windows. I know at one time that 3DC did not remove that folder when you un-installed.
You will have to re-register your serial number again by removing that folder.

Yes that would be good to have, Select one polygon and then press R or L key to select the different kind of loops.
For now I use the Lasso tool from the E-panel to select multiple polygons to delete when I have "Select" chosen in the Left tool bar.
Deselect Auto in the top tool bar and choose Faces instead.
Select the polygons and then use the Delete key...
 
Second method:
If the tip of the fingers polygons are disconnected from the rest of the mesh, In the left tool bar select "Del. Polygons"
Now hold down the Ctrl key and hover over the disconnected polygons. All the finger tip polygons will be highlighted.
Click your left mouse button to delete them. If you are using a tablet, just press the tablet pen to the tablet after the polygons are highlighted to delete them.

I tested the test.stl file. It imports correctly.
Your problem is that you have "Import w/ Thickness" selected.
It is not needed for closed objects. What you are seeing is the thickness proxy...
Also make sure symmetry is not turned on...
 
For objects that are no closed, The green is your thickness proxy indicator, a visual feedback.
Same principle as adding thickness to flat plane polygons in a regular 3d modelling application.

What version are you using...
4.1.17D and the 4.5 beta now have a separate Bake menu. The settings are no longer under Retopo menu.
 

The shadows are not being baked in... I do not use VRay so I do know how to setup for PBR rendering or how well Vray supports PBR rendering.
Check your settings in VRay and the export settings in 3DC.
I use the Roughness / Metalness export.  There are 3 export methods. 2 are for PBR and one is I believe for the old way of using a regular specular map if you desire to render the old fashion way but that would not a true PBR material. I could be wrong on that, I have not tested it.
 
Also in 3DC view menu, you have 3 type of shaders to view your model. I use GGX.
 
Now In Blender, I use the PBR shader connecting the right texture nodes to the correct input nodes... 
Albedo, which in 3DC is call color in the export settings.
Metalness
Normal map
Roughness
I do not need a regular specular map as that is not needed in a PBR setup even though it is included in the Blender PBR shader.
I get pretty much get what I see in 3DC's viewport in my blender render according the strengths of my light setup. In my scene I have a fairly strong hdr image adding light to the scene and a sun light so my ball is brighter than in 3DC.
 
Note: I answered your question about auto-retopo in the thread you posted it in if you have not read it yet...
 
Just in case you have not read this information before...
http://www.marmoset.co/toolbag/learn/pbr-practice

If you are rendering for Ptex in your renderer (like Renderman) export your ptx files for color, displacement etc through the textures menu. shown in the second picture, the textures export picture. Be sure to choose exporting for ptex not the regular color or displacement etc. It will create the one Ptex file with the extension of "ptx"  There are no image files exported in the Ptex file format like we get when exporting for regular color, normal or displacement maps.
 
Next,under the file menu export, just export the low polygon model, nothing else.
 
If you have combined all the ptex maps to one map using the Texel tool panel and want a regular color and displacement map then use the file menu export options. Export out your color and displacement etc. Here you are not using the ptex format, there are no options for it in this export panel.
 
EDIT. From my testing the amount of ptex maps created by default when importing for Ptex appears be more due to the amount of internal millions of polygons that 3DC uses to create your displacements. Shown in picture...

It was my fault, Carlosan, there is no need for arumiat to send the file. I was using Beta 12 when I told him he could bake the vertex colors. arumiat is using 4.1.17D. He will have to installed the Beta to be able to bake his vertex model's AO. I do not every day used all parts of 3DC plus the betas, my mermory failed me this time.