It's possible that the boot manager is confused about what to use as root fs. This gets slightly more complicated if you are using SATA and old IDE disks together. In any case, your best bet is to play yourself with the boot manager and see if you can find something. How to proceed will depend on wether you use LILO or GRUB. In grub, you can press 'e' to edit the root and kernel line(s). Grub specifies the disks as hdX,Y, wheren X is the disk number and Y is the partition number. The disk number will depend on how the BIOS orders your drives. The good part is that if you edit the boot lines, you can just erase the 'X,Y' part and then use tab completion to see what's available, and try to guess what's the correct disk and partition pair. Once you've managed to boot you can fix the changes in /boot/grub/grub.conf or menu.lst, of, for grub2 in grub.cfg.
This is a guess on what your problem is, I can't really say for sure since I have no real info to work with.