Oh boy, this sounds awful (and gives me unpleasant flashbacks)!
Are you aware of the following thread (the issues, random source code changes leading to different results/ crashes, file format stuff)?
http://www.opserver.de/ubb7/ubbthreads.php?ubb=showflat&Number=458100#Post458100Which engine version are you using, 8.47.1? If you don't... you should.
Do you use view/ sky entities? If so, how are they created?
Do you use default acknex sounds? Have you tried disabling them (-ns)?
About plugins: As I may have said before at some point I once managed to really mess up my game, having all sorts of random memory issues, inexplicable behavior and random crashes, because I sent a NULL string to a Steam API function on accident which really did not like that. I assume you've been experiencing those issues way before you started with the Steam implementation, right?
