This is the last part of my build and it's driving me nutts.
I have a Toshiba Samsung TS-H652 DVD-RW drive, and I can't seem to remove the mounting screws (used for the quick removal slots in bay). When I unscrew them there is NO tension, they simply spin in place.
The are 2 holes adjacent to each screw ... my guess is that some sort of tool need to be stuck down there to brace the nut so I can unscrew it.
I stuck an awl down one hole, and was able to remove ONE screw, but the same technique did not work on the rest.
I don't think that you are being stupid; it is not uncommon to find the wrong screws being fitted in the wrong size/thread holes in home built systems. However it is unusual to find this on pre-built assemblies from a manufacturer. The solution you used to remove the screws is good if you can get it to work as you need something to push the screw up while turning the screw. If you can't get something under the screw then an alternative solution that I have used is to use epoxy resin to glue the screwdriver to the top of the screw and letting dry overnight being careful that you don't use to much so as to glue the screw in the hole.
Is this a brand new DVD drive? I've never seen a drive that comes with the screws already in the drive itself, the screws I've seen always come in a separate tiny plastic bag. So are you talking about the screws that go into the drive itself, or are you talking about screws that hold the quick release rails into the case, or something else?
Are you sure you're working with the screws that are used to secure the drive to the drive bay (or quick removal rails) and NOT the screws that hold the DVD drive together? You should NOT have to remove the latter. No drive of any sort that I've ever seen uses an internal nut for the screws that secure the drive to the drive bay.
Did the screw you successfully removed have threads on it? When you removed it did it leave a loose nut rattling around inside the drive? If so, then I suspect you've removed the wrong screw.
This diagram shows where the holes are for the screws that fasten the drive to the drive bay or the quick mounting rails. This diagram isn't for a DVD drive, but the shape of the drive and the relative location of the mounting holes will be the same (see the arrows indicated by  and ignore the ):
Assuming we're talking about the correct screws, if the screw heads aren't flush with the surrounding sheet metal then you could try gripping them with a pair of needlenose pliers and using a rotating-pulling motion to ease them out.