Zeke, if I had to guess I'd say your motherboard is garbage. I have an S3, same basic thing as you and I've been having disk access problems for several months now. My old SATA drive died after a reformat, I couldn't get XP to install w/o blue screening. Took the SATA drive off and used an ATA drive and got XP to install, but everything is slow as crap in Windows. I get flashlight while opening folders to show files, it takes like 45 seconds to empty the recycle bin even if it's only got one or two programs in it, horrible load lag and FPS in games, etc etc. You're the third person I've talked to with a P965 based Gigabyte board to express problems with file system and memory related problems, I think it's safe to assume at this point that there's a common theme in our motherboards. Hell I can't even get my floppy drive to work anymore, shows up as A: in Windows but won't detect when a floppy disk is inserted, so I can't even Bios flash.
PS. I've done multiple reformats, so this isn't a virus or spyware screwing me up, we're talking completely clean windows install and nothing else, and things are still fubar with multiple HD's being tried.