If you're just now getting around to upgrading to 5.6, and your machine running 5.1.2 or 5.5 has been exposed directly to the Internet, your machine is most likely compromised. Best procedure: use a Knoppix CD to save your data to a networked share or a second hard drive, then reformat & reinstall with 6.0.1 (or wait for the first Lycoris release).
Alternatively, it may be that your hard drive is corrupt, in which case use that Knoppix CD again to do a fsck.
But I'd bet on your machine's having been r00ted.