I think the latest Nvidia drivers (177.83) help some; I can start and spawn fine now(as Rebel) and even turn the 3d icons on and off but as soon as I come into range of the 3d icons for the deflection towers I get the same glitches as before if 3d icons are on. Maybe you could try changing the 3d icons for the towers to something more basic and see if that solves it.
Second, if you'd rather stay in your native resolution, right-click on your FirstStrike shortcut, and select properties. Then in Target box, add +szx 1440 +szy 900 to the end of it (REPLACE 1440 & 900 WITH YOUR NATIVE SCREEN RESOLUTION)
It should be noted as we now have the launcher the properties go to "Arguments" under File>Preferences in the launcher