Sounds like the MFT might be messed up - have you chkdsk'd or fsck'd the drive? I hope you still have the original data elsewhere. Moreover, with drives that large i'd suggest using a more advanced filesystem like ext2/3 (or NTFS for compatibility. you can use ext with windows but it can be bothersome esp if you intend to use vista). Filesystems with journaling and built in security features are superior to your avg FAT32 setup in my humble view.
If your MFT and FAT are messed up and you've been writing files to the drive, be prepared for data loss. a recursive disk recovery tool like r-studio might be able to pull most of it out, but overwritten data is hard to retrieve. See if qtparted/gparted/parted see the data on the partition and try to pull it out that way if you have no backup too.