Comment 182 for bug 346691

Marco, there is a known hardware data-corruption issue in certain revisions of Via VT82C586A/B/VT82C686/A/B/VT823x/A/C disk controllers; this is most likely the issue you're hitting.

I'm not aware of what workarounds exist. To confirm the issue is with this disk controller, mount the internal 2.5" harddisk in a USB enclosure, boot off it and see if you can reproduce the issue via USB, and you'll know.