No way would I like you to treat what follows as a certain answer, but I often get help by just chucking ideas about.
Over the years I have had drive letters turning up in unexpected sequence.
In SCSI days this seemed to have priority over second HDs which were IDE. Maybe the same thing happens with SATA and IDE, but I don't know?
You haven't said wich OS you are using, I assume it is XP
Is there a mismatch with say an OS formatted on FAT32 and other drives as NTFS?
As I said this is not an answer, just a few (I hope helpful) ideas.