Well, I wont say much about this computer I'm dealing with, needless to say I can't modify the hard drive contents and I don't have access to the internals.

Booted up a copy of BackTrack 4 Final onto a computer after acquiring BIOS rights. We got the password to the BIOS, changed the boot order to CD and first booted to windows normally. Then we restarted and booted into BT4 to see what we could do. I got called away and when I came back my partner in crime was pale and was looking at the BIOS. The first HDD was no longer in the BIOS boot options, we get an error (more info on that error later) when we don't have a disk in the drive.

Loading up BT4, the hard drive is still visible. It's just not being picked up by BIOS.

Tomorrow we'll be playing around, our ultimate plan is to upload a back door, fix it and give ourselves remote access from our own computers, though if it goes on erroring out like this the HDD and BIOS are sure to be flashed.

So... Any idea what might be doing this? Any BIOS settings or even a linux setting that may have somehow played with the hard drive?