I have a relatively new PC running XP Professional with SP2 after removing Vista Home Premium about a year ago.  For the past several weeks I have had a strange thing happen to the hard drive boot sequence.  I have three SATA drives, and boot from the first.  But now the sequence in the BIOS has changed by itself or some unknown cause about once a week.  The motherboard is a Gigabyte S-series.  When I find the wrong disk is attempting to boot and failing I reboot and reset the BIOS to the correct sequence again.  I run Trend Internet Security Pro's antivirus and use anti-spyware software and Diskeeper defragmentation.  But, I wonder whether I might have some kind of spyware or rootkit resetting the HD sequence.  Otherwise, what can be causing this?

The odds are that the priority is not changing, but rather you have a problem with your primary drive and the bios cannot always access it properly and then moves on to the next boot device. Reseat your connectors to the drive and stress check your hard drive as well as your registry.

Might be worth a battery change. Inexpensive and it wouldn't be the first time a new PC has needed one within a few months.
Nick

It sometimes pays to ask the obvious. When you make changes to the bios are you careful to hit "save on exit"? If you just exit the changes are not saved.