Ok, I gave it all night once (about 8 hours) to shut down, and it didn't. I've even reinstalled windows, and it is still giving me the same problem. It works initially, but as I install more software and drivers, it takes a little longer each time, until it stops working all together. At first it worked when I shut it down from the start menu, but didn't when ever a program shut it down (I don't understand why). I've tried shutting down from the command prompt, using various different combinations of switches, and that didn't work either.
The only difference in software between my old hard drive configuration and this one is that I'm running the Catalyst 5.8 drivers as opposed to 5.7. But I have a feeling, if that was the problem it would be all over the net.
No aspects of this problem seem to make any sense at all. The primary array does seem to be a little flakey, if I don't run the SATA cables just right it will error on boot. When I get back to school, I'm going to buy some new, (and much shorter) SATA cables, and I'll see if that has any effect on the problem.