Hi,
next time when you want to swap the drives. Stop the backup exec services and then swap the drives. and start the backup exec services.
can you confirm if the drive letter assignment has always been a issue or is this occuring oflate. If you are seeing this now then the issue might be that the disk headers (0 sector) which has the partition information is getting corrupted. There might be some conflict which is causing the drive not being assigned the drive letter correctly.
the issue might be more with windows than backup exec
bhanu