This engine's save system basically serializes a copy of the entire map + whatever is going on in it at the time. Naturally, in EXU, this means it saves a TON of info. Sometimes, the engine just shits itself. Unfortunately, I have no idea what conditions actually cause this to happen, but it's usually when a lot of stuff is going on all at once.

1. When you notice saves are broken, open the console (press ~ or Tab) and type "showlog"
2. If you see an "error moving Save.tmp to Save##.usa" somewhere, Save##.usa is corrupted
3. To fix: save your current game in a different slot (or in any normal slot if your Save1000.usa, which is the Quicksave, got corrupted)
4. Close UT and open your ..\UT\Save\ folder
5. Delete Save##.usa, where ## = the number of the corrupt save
6. Reopen UT, load your functional save, and save over the now-dead slot (there will still be a name here)
7. Try saving again in that slot and it should work. Hooray

I know this is kinda shitty, but it's the best I can do for now!

To avoid this issue, make a save in a new slot at the end of each map before you load the next one. This way, save corruption won't take you back so far. I also recommend starting with a clean slate before you play, i.e. no save files at all. But saves from other map packs should not impact EXU at all, nor should EXU affect them.