I just started playing FNV this week, and I'm having some issues already. Here is my system, which is heavily watercooled:

Case: Cooler Master HAF X RC-942-KKN1
Power Supply: Silverstone ST1500 1500W
Motherboard: Gigabyte GA-X58A-UD9; CPU: i7-980X 6-core @ 4.16 GHz; Memory: G.Skill Trident+ Turbulence II 12GB (3 x 4GB) DDR3 2000
Graphics Card: 2 x XFX ATI Radeon HD 5970 2 GB
Optical: 2 x Lite-On iHAS424SATA 24X DVD
Hard Drive: 2 x OCZ Vertex 2 180GB SATA II SSD
Monitor: ASUS VH242H 23.6" 1080P LCD; Colorvision Spyder3Elite Calibration

The main problem is that whenever I run any program before FNV, the entire screen flickers; this happens during the intro, on the title screen, during play, etc. It is annoying enough that I can't play it. If I boot up and don't run ANY programs, this isn't an issue. It's just a pain having to reboot every time I want to play, and I also would like to be able to run a FPS monitoring program, which I wouldn't be able to do, because I can't open up any windows without encountering flickering.

The other problem (and this happened when I had rebooted and wasn't getting the flickering) is that the opening video (after you start a new game) had horrible stuttering. I gave me a headache watching it; a ten second section of it would usually take about thirty seconds to play; the video would freeze and the audio would sound like a skipping CD.

Here's an update: if I run it in windowed mode, it never flickers, whether or not I have run programs before it. Come on, somebody help me, please!

I had similar problem, try resetting your monitor to factory defaults, also reset the color calibration in the CCC.