Freakin flickering

When I first played Doom3 about a year ago, it ran fine at basic settings, the only thing that really annoyed me was a horizontal flicker that happened when opening the program at the beginning scene (ID software logo). This flicker didnt occur during gameplay, but it also happenes during the "wormhole to hell" clips in between transports. Fast forward to today, I now have the best video card that can go in my system, and gameply is great at max settings, this flicker still occurs though!!! Only during pre-made scenes, not gameplay. Any ideas?