Boot Camp on MBP internal drive (disk1), attempts to boot off CD bay drive (disk0).

Hi. I have an early 2011 MBP running the latest version of Mavericks with two internal SSDs. The HD bay has a 1TB (disk1) and the CD bay has a 512MB (disk0). Boot Camp is installed on the 1TB. When I boot up the system and hold down the Option key, I see Windows as a boot option. If I select it, however, it starts to boot and then goes immediately to a black screen with a white underline cursor blinking in the upper left. It remains like this until I reboot.
After spending a lot of time looking into the cause of this problem, I've come to the conclusion that the system is confused by the drive in the CD bay and is attempting to boot from it before it attempts to boot off the drive in the HD bay. I installed Boot Camp originally by using Boot Camp Assistant to partition the drive and then using WinClone to copy over a previous Boot Camp partition. I'm pretty rusre that as a result, one of the following two things is happening:
Whatever setting Boot Camp Assistant made to tell the Windows install DVD to boot first is still in effect and Boot Camp is attempting to boot from the CD bay.
The Boot Camp partition is set from the previous drive it was on to boot from disk0, which is now being assigned to the drive in the CD bay.
To test these theories, I've unplugged the drive in the CD bay and rebooted, at which point Boot Camp boots perfectly off the drive in the HD bay.
The drive in the CD bay is set to a single HFS+ partition. I've looked at the GPT and MBR on both drives and they seem fine (the Boot Camp partition is bootable). Does anyone have any idea what I'm missing here?
Thanks in advance.
Craig

Still having issues, any suggestions would probably be helpful.

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