I'm having the same issue with save file corruption as well. I've also spent 10+ hours in Fort Joy speaking to people, stealing from some. This started happening to me after I got my collar removed and fought some of the magisters. Might be unrelated, but several companions got the permanent Wet effect as well.
At this point, it would take around a minute to load the courtyard of Fort Joy in front of Lucian's statue. As I progressed a little after this, the game just froze around this area without successfully loading it. Memory usage went up to 99% (the game used about 10GBs of it), while HDD I/O and Paging errors increased considerably.
It's just a guess, but it seems that this bug started happening after I stole some stuff and ran away without ever letting the NPC I stole from confront me.
Also, it seems to me that saving without pausing the game in the meantime is just asking for trouble...
