Long story short, still having the problem :S
I did chkdsk, fixboot and fixmbr (it wouldnt take fixboot /mbr? but it did the same thing). Chkdsk found a couple of errors but fixed them, and I rewrote the both the boot sector and the MBR.
So on to diagnostics - I've been running a SMART checker for a few days, and I ran both the short and long (bout an hour and a half -_-) versions of Hitachi's Drive Fitness Test. Both came up 100% clean. The SMART tests have been perfect except for an occasional jump in seek error rate.
Any suggestions on where to go next? I'm completely out of ideas...maybe I did something wrong? I've never had SATA before - but it did work fine for Windows install, etc...I'm using it now, through the 'select OS' screen.
** By the way, sorry if it takes me a few days to respond - I work and go to school so I dont have a lot of time to even work on this