Thanks to Component Actual for this fix:
Thanks for the advice, but I deleted the textures you suggested (the grnd folder) and tested and it still had the weird black polygons and then I tried deleting all the shaders as well, but it didn’t help either. So as a last ditch effort I checked Nvidia’s site and got the latest BETA driver for the GTX 480 installed it and left everything in the Nvidia Control Panel at their default settings and just like that no more black polygons.
However, when I exited the game and went back to the Nvidia Control Panel and changed a few settings the problem reappeared. I was eventually able to narrow it down the Antialiasing of Transparent Textures. If that setting was set to "on" in the Nvidia Control Panel then I had the weird black polygons if it was off no problem. So really I don’t even know if I needed to change my driver or not. So if anyone else is having this problem turn off transparent antialiasing.
Just for the record I am now using the geforce 260.89 driver.