Macbook Pro With Second Drive - Black Screen White Cursor when Booting?

I have been looking around for someone else with this specific problem with a macbook pro. I am wondering if anyone from The Verge has encountered this bootcamp problem and come up with a solution.

I have a 2012 13" Macbook Pro. I took out the optical drive and installed the following set up:

128 GB SSD in hard drive slot

- Single Partition -

Format: Mac OS Extended (Journaled) - Mountain Lion Install + Applications and select User folders

750 GB OEM HHD in optibay enclosure

- Partition 1 -

Format: Mac OS Extended (Journaled, Encrypted) - User Data

- Partition 2 -

Format: NTFS - Windows 7 Enterprise Install

You may already know that it is difficult to get Bootcamp and Windows 7 to install on a hard drive in the optibay but I got it to work by using a external hardrive . I opened up the Macbook and disconnected the SSD from the motherboard. I used the OS X install on the external USB to boot and run boot camp. Boot camp created a install usb stick from an ISO of Windows 7 Enterprise (to which I have a legal license) and created a partition for Windows. I went through the reboot (be careful because before you restart you have to unplug the USB hard drive with OS X) and installed Windows 7. Everything worked beautifully and the installed great. I installed programs and rebooted several times with no problems but when I plug the SSD back in and try to boot into Windows 7, I get a black screen with a blinking cursor. I can boot in to OS X just fine, from either the SSD or external drive but not Windows 7. If I unplug the SSD, I can get Windows to boot just fine. Is there anything I can do to get both OS X booting from the SSD and Windows from the HHD. Thanks for the suggestions.