I uninstalled the game, deleted the Program Files Academagia directory, added DLC 16 again, and now everything seems to work. Don't know what the problem was, but I'm now able to overwrite files again, so it looks like it might be fixed. I'll let you all know if it crops up again, but thank you for your help; I think it might've been when I put in DLC 16 for the first time, since that's when it started happening. Thanks for your time.
I couldn't find anything on the forum regarding this glitch in 7, so figured I'd post it here. I appear to be getting the Vista save glitch (overwriting save files causes them to disappaear, new save files don't save) to a ridiculous degree. I'ts not uncommon to have to exit and reload the game at least twice before successfully saving anything, and by midterms I've had more failed saves than successful ones. I've tried uninstalling .NET framework 4.5 in the hopes that 3.5SP1 would take over, but no dice. I'm aware this problem hasn't been solved for Vista, but if anyone has any insight on how to fix this aggravating thing in 7, it'd be much appreciated; it's hard to enjoy the game when you frequently have to redo days or weeks three or four times.