Here's a guess:
I have noticed that when BIOS LBA-detection is on "auto" then often BIOS and Linux will have different ideas about the drive geometry.
Linux seems to use LBA as default, the BIOS in my computers use "large".
To try it, do this:
1.) Run setup, write down the harddrive settings. LBA/large, number of heads & cylinders.
Do not change anything! You might ruin everything on the drive!
2.) Boot a live-CD. Check with fdisk:
# fdisk -l
What does it say about your disk? If the geometry differs from BIOS, enter fdisk and change them:
# fdisk /dev/hda
Use 'm' for menu, I don't remember where you change heads, cylinders etc.
If the settings are identical, the problem is somewhere else. Currently I have no other ideas.
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