as you may have an open mind on these matters can I talk thru 2 suggestions
1) bios boots to old windows to old mbr which needs a bootloader to boot both drives
2) bios boots to second drive mbr with a bootloader to boot both drives
It is not clear to me which is your bios booting to from your post.
grub can boot any but you may need to be sure what is what when installing the new distro.
and highly likely you need to install a bootloader like grub on your preferred bios boot drive.
http://www.linuxquestions.org/questi...hreadid=237511 may help
if probs post your type of drives like IDE/scsi/sata and if not sata what is primary/slave and what bios boots to first please.