I ran the multiple instructions for getting a clean install of FS X + Acceleration and the OS cleanup/tuning found in multiple posts around here. I downloaded the 8.5 version of O&O Defrag that I found a link to here and used that as instructed. Everything seemed fine after I was done and FS X ran nicely, but I noticed when I went to download an AVI file demoing TrackIR Pro I couldnt save it (got a file name error). I didn't think anything of it and went to bed.
Today after I get home from work I found several pop-up error messages about C:\$Secure being corrupt. I did some Googling and found some people who had this after installing IE 7 and their system was stuck in a chckdsk loop, but I've never installed IE 7. I also tried to download some more things in preparation for a possible rebuild but again noticed I couldn't save any files, I'd just get an error saying the filename wasn't valid. I tried to reboot but found I was also suck in some sort of loop (looks like chkdsk tries to run but it goes by very fast before rebooting again), so I tried to go into safe mode, but that doesn't work either. I suspect that the O&O offline defrags somehow messed up my MFT ($Secure lives in the MFT). Maybe the version I got from www.b3ta.cr3ation.co.uk isn't what it seems.
I can't think of anyway to fix this without a complete wipe and rebuild, which is not going to be fun at all. Though I will be getting a new hard drive and use this one as an FS X only drive.