That's incredibly bizarre and I have no idea how to fix it.
But man nice job with the video card!!! Have you tried installing MTAEVWD's extra unoptimized rocks and stuff to see if it runs at like, 4 fps instead of 2 fps? That's what I'd do if I got a beefy new card. You've got me looking at video cards on newegg now, drooling and jealous considering I built this computer two years ago. Telling myself I can splurge after Skyrim comes out, no use in getting anything now, but those 6950s seem pretty nice for the cost... Dammit!
Sorry, easily distracted and often derailing. New video cards get me excited, though, living vicariously through others and all.
Anyway, I'm assuming you've uninstalled/reinstalled Gecko, rebooted your computer and tried it, all of that stuff? Hmm, have you tried it while using a different screen resolution? Ran it in compatibility modes? Just trying to think of anything you can do, that won't necessarily fix it but could at least providing some insight.. Hmm........