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.

-- 
2.6.28-11 causes massive data corruption on 64 bit installations
https://bugs.launchpad.net/bugs/346691
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