Cause it sounded like you had an install problem? I don't see why, if you have them both installed correctly, that they can't work. Though I will say that if you use repair windows it will install on every MBR that it can, or at least it has issues when it comes to this. It has the bad habit of installing on the MBR of other discs. That's why when I install windows I always unplug my linux drives, just don't like fixin it.
If I were you, I would get each drive booting with all the other drives unplugged so you know you are getting the correct drive. THEN if you get errors I would report it.
So if I unplug my Linux drive and repair install Windows, then plug my Linux drive back in... Windows will work when I select it in GRUB?