So after doing some playing around, swapping between full-screen and windowed mode seems to be the actual issue.
So for example, Swapping between the commands “setres 1024x768f” and “setres 1024x768w” causes the issue to happen.
Specifically on the window mode the game did NOT start in. (so if we started in full-screen, then windowed mode has offset issues.)
I’m guessing this might have something to do with Linux not handling Full-screen correctly. (I’ll enter it as another bug.)
Also forgot to mention in the original bug that i’m working on Ubuntu 14.04 LTS.
NOTE: This is easier to see if there is a button highlight on hover over (Something we have in our game)
Hope that helps. 