Bootcamp, optibay SSD, blinking cursor.

December 2012 MPB 13".

Installed Windows 7 pro on the OSX disk, which is an SSD in the optibay. Everything went fine installing via bootcamp and USB except the installed couldn't see the SSD as a boot drive if the other drive was installed, so I unplugged the second drive and installed. Windows is up and running normally, can swap between OS's easily. Everything seems hunky-dory unless I plug the second drive into the main bay. Then windows refuses to start, giving me the endless blinking cursor. Unplugging the second drive allows windows to boot normally.

Everything I've read seems to indicate that this should work. Nothing changes other than mounting the new drives. The SSD remains as disk0 and the new drive mounts as disk1.

Have tried many different things, in windows, windows RE from the USB, and os x. Windows RE says there is a partition error, but fixing it does nothing. Setting the active partition via various partition utilties like fdisk and Diskpart either does nothing or white screen at boot.

In windows RE, bootrec.exe /fixMBR works, but /fixboot and /rebuildBCD come up with the error "element not found".