The system boots to the first active partition it comes to via the boot priority. If there was no active partition on the second hard drive and you set it first, the system would still go to the active partition on the other drive.
If both drives were set to boot (active partitions containing boot files), you may be able to use the F12 key (depending on your system)to choose another bootable device.
I have also seen situations with clone drives that messed up the Drive letters, so the BCD store might still be pointing to C: with the clone being something else.
A snipping tool picture of your Disk Management might help. You could attach it using the paper clip on Advanced replies.