I recently ran into a very similar issue. Windows, or at least Boot Camp, will not boot into an HDD that is installed in the optical drive bay. I do not know why this is, or if there is a way to fix it; all I know is that as soon as I moved my HDD back to the HDD bay, Windows started booting again.
Boot camp has many issues with MacBooks whose optical drives have been replaced, which are well-documented on the web. This article (and its comments) describe many of them, and the workarounds that people have found for them. That said, I think that Boot Camp has improved with Mountain Lion (or possibly with the continued proliferation of optical drive-less machines from Apple), because I was able to boot the Windows installer just fine from the optical drive that I had removed and placed in an external USB enclosure. (Not that it did me any good - I received the dreaded error 0x8030024 when I tried to actually install Windows.)
What worked for me was to install Boot Camp before removing my optical drive, use WinClone to make a copy of that installation, and then clone the image back to the drive once I'd gotten my drives in place.
So, in summary:
- Try putting Boot Camp on the drive that's in your HDD bay.
- The article I linked describes many of the issues you might run into and provides workarounds for them.
- Worst case, you may have to reinstall the optical drive in order to install boot camp, then use WinClone to move the installation to any drive you wish. (Hang onto this image for all future Boot Camp installations.)