I'm not sure if this is coming from my video card, Faark's mod UI, or smart-hide. I love smart-hide and consider it essential, but may have to stop using it for now.
I like to play in windowed mode so that I can chat while I'm going. Since I started using Faark's mod to run smart-hide (which is the only mod I have enabled) I've found that if I click on another window and then click back on Gnomoria, the game no longer detects my mouse position correctly. It's typically off by about 2-3 inches on the screen, with the game registering my cursor as being that far above where I can see my mouse pointer.
I've run with this same windowed resolution on non-modded Gnomoria and have not encountered this problem before.