M2A-VM disk boot order?

I bet there's a cure for this, but I haven't seen it yet: any disk on
the IDE controller is automatically considered C:\, or the primary
disk+partition, when installing a windows OS, so when I put win on the
first SATA drive, it's always listed as D:\ if there is an IDE disk
attached. Don't know if this is true with linux yet.

When I added a second IDE drive, my SATA windows install, on primary
and active partition 1, suddenly was considered to be on disk 2 (of
disks: 0, 1, 2), so it wouldn't boot till I rewrote the boot.ini That
reduces flexibility a lot; I'd like to be able to move my legacy
drives around and exchange data while rebuilding my test + low volume
server with the replaced gear.

I set the boot disk order in BIOS, but that only seems to affect where
the bootloader is look for.

/..