I experienced a somewhat similar result when I changed to a larger (first) SATA drive in one of my other XP machines about twelve months ago. The bios assignment of the newly cloned and bootable SATA drive when compared with the previous IDE drive was confusing (to me), and not what I expected or really wanted. However I was unable to really change it, and because I didn't have the time to persevere, I left it as it was intending to sort it out later. After all, the machine booted from the required drive, and I was able to assign the desired drive letters within XP, even though the bios saw things differently. Strange, but it's a computer after all ....
Over twelve months later I realise that it's turned out to be a reliable system, and I had virtually forgotten about the matter until I stumbled upon this thread a couple of days back.
I think that if you can live with the apparent anomaly, and you assign the drive letters which you require within the OS, the machine will probably continue to do all you require of it.
FWIW
FOR