I wonder if all this crashing and file writing-overwriting has anything to do with Permissions??? Try running the .exe "As an Administrator" and see if that solves anything. You could also try installing the game somewhere other than Program Files or Program Files (x86) folders or even root C:\ directory. I install some things into C:\Users\"Username"\Apps, where Apps is a folder I made for random programs.

My friend and I have been playing co-op ever since v1.0.36 original release and neither of us has experienced a SINGLE crash in neither Co-Op Mode nor Single Player Mode. He has a 3570K @ 4.4Ghz, R9 290 (overclocked), 8GB RAM, SSD, Windows 8.1 Update 1. What I have is in my sig.