LOL, and just after posting, I figured out that the problem was Firefox! Who would have guessed... I assigned a custom setting to Firefox in my Wacom settings and set the screen projection to my main monitor, and the problem stops now to occur in 3D Coat. How weird.
I always have firefox open as I listen to a lot of music on YT while working. Seemingly Firefox interefered with the mapping globally, causing the issue to happen in 3D Coat. I believe, each time when you enter a number in 3D Coat into a menu entry, the menu gets modal and 3d Coat sleeps in background, and hence the Firefox context was somehow active while dealing with the menu while entering a number. Setting Firefox also to single screen prevents it from messing with other apps. I have no idea why it was this way now, as I worked for years without this issue. Who knows, maybe some firefox update caused the issue, especially since they added editing PDF and stuff, I reckon they also worked on their pen support, potentially unwantedly messing with the driver. Usually, the "all other" in the driver set up setting should have taken care of it.
Then again, maybe I did add a custom firefox profile at some point without noticing. In any case, pen in 3D Coat works just fine as always!
Henry Townshend's post in Live Booleans Collapse not working was marked as the answer