I know this one.

First a disclaimer - 3.9 is still alpha, so not really stable enough for normal use.

Anyhoo, 3.9 can cause a crash upon exit - it's to do with RTRT.

Your screen's going all weird afterwards because the OS isn't restoring the desktop resolution when the game exits, and is stuck at the resolution Toribash was running at. The rest of it is basically Windows being all "WTF JUST HAPPENED?!?!?!" and refusing to behave afterwards, so I present to you 3 choices to fix the issue:

1. Don't use 3.9 for general use, it's only a test version after all.

2. Don't run it full screen, if it crashes when windowed you'll not get the cocked up desktop issue.

3. If you must use 3.9, and must use it full screen then set the game to run at the same resolution as your desktop. That way you get full screen RTRT & if it crashes your desktop will still be intact. Be aware that it'll run slow as hell if you have a high res desktop.