I've been noticing some very weird glitches in cw3. Admittedly, this is while trying to do something ambitious with CRPL and there have been cases where doing a particular thing in a script breaks the game. Things like command nodes turning completely black when the camera is in a certain position, units in an area being invisible, and the UI being invisible or buttons hanging off the screen and overlapping after SetAlternateControlMode(false).
These could be due to changes between unity 4 and 5. It could also be that the version on the main menu is "2.12 Steam" even though I don't use steam and downloaded the game directly from KnuckleCracker.com. It could also be due to my GPU starting to go bad.
I have downgraded to 2.08 to see whether the problems persist, to rule out the possibility of a hardware issue. After about an hour, thus far they haven't.
I have no problem except sometimes the ammo bar of my guppies is shifted right by about 10 pixels. Only on loading old games, but it rectifies itself after they launch again.
That steam text in version number is normal thing there.
Sound like GPU driver problems that might be amplified/exposed by Unity 5. You are on linux too I think... so that's an extra variable. I'll be building CW3 with the latest Unity soon, so you can see if that makes any difference.