Interestingly enough, I had problems with Windows 7 (as well as Windows 8) restarting with some external HDs attached - three different ones, actually. After reading your note, I wondered if the issue with the failure of Windows 7 to restart might have to do with the fact that the HDs were attached. I ejected them in OS X and then tried a reboot - Voila! There was Windows 7, all happy again.
With respect to checking to see if the HDs are boot options, OS X (I'm using 8.2) does that prior to an OS comping up. If you hold down the Alt key while Boot Camp is restarting the Windows and Mac disks come up along with the Mac Recovery partition - not the others. So it already seems to know that they're not bootable. The problem might be that Windows is trying unsuccessfully to wrest control of those HDs from the Mac OS. What about it all you techs out there? Any ideas?