WARNING!!! NERDY POST... BEWARE!!!
Through a combination of interactive fsck,vfat, custom perl scripts, and manual renaming of directories/files I seem to have restored a partition to a nearly pristine state. It has been causing me problems for around a year. I bet I could even get it to boot now.
Oh, and I seem to have fixed the problem with mounting samba shares causing nautilus to immediately crash, mount, and smbmount, and any program that tries to access the mounted share to become hung, and unkillable. It wouldn't happen if I mounted the share read only. I really don't know what I did to break it or fix it. It might have just been doing an update with apt since it started after I updated, and ended after I updated, but I didn't see anything about mount, or samba in the update. I also guessed that it might have something to do with a bug in a kernel module because I added a few things to what get inserted at startup so I removed a few, but I think that isn't what caused it. I really don't know. I'm hoping it was a bug, and it got fixed that way it isn't my stupidity. :-/