If you're still having the issue, the issue is likely caused by the motherboard, main board that everything plugs into, not finding the hard drive with windows installed.
Firstly, try removing any USB devices, (keyboard, mouse, USB Storage) then reset and try rebooting.
Assuming that doesn't fix the issue, you'll need to replug the keyboard and mouse in and change the boot order of the drives around, or force boot from each drive to see which, if any, goes to windows. Difficult to say exactly where this option would be for you, as all motherboards show this slightly differently.
If this still doesn't fix the issue, you may need to open the machine up and see if any drives are disconnected, or have loose cables.
Failing that, it's difficult to really say remotely sorry.