I have had this problem several times and I don't know if I am doing something wrong. But sometimes I like to open a new project file and create some geometry and paint it via
vertex colors. and when the object is ready import it into the main .3b file with the larger scene, keeping the paint layers.
But several times I have noticed that the paint layers don't all show up after import. On this occasion turning one of the layers off and on, fixed that one layer, but didn't for the rest leading to me believe that their is a glitch in the code on import like this.
However I am not sure it is a setting that is conflicting with the geometry. Which could be possible.
If anyone knows what this could be or it is a glitch, it would be very helpful