The point is it's not a Windows issue! ;-)
I would change the boot order in the BIOS. If the BIOS is set to:
1. USB
2. HD
3. Optical
Then re-arrange them to have the HD at the top.
If on the other hand it's already in the correct order, I would take a look at your HD's. Maybe they are damaged? (Are you using RAID?)
See if the HD's are being recongised in the BIOS during the POST Checks.
Good Luck,
Steve.
"They have the internet on computers now!" - Homer Simpson