Do the following in order:

1. Download and install the latest nVidia drivers (270.61) as well as the latest SLI profiles.
2. Turn off your computer and disconnect it from all power sources.
3. Open your case and ensure your SLI bridge is connected securely. Also check that all of your hardware's power connectors are securely in place.
4. Close your case.
5. Connect your monitor to the GPU in the second PCI-e slot. Make sure it is connected properly.
6. Boot up your computer and go to the nVidia control panel.
7. Under "Manage 3D Settings", select the program settings tab. If you do not have a profile for Crysis 2, add one by browsing for the Crysis2.exe file in the bin32 folder for the game.
8. Set the SLI Rendering option to Alternate Frame Rendering 2. Apply changes and exit the nVidia control panel.
9. Start Crysis 2 and play SP and MP flicker free (even with v-sync disabled!)

I had tried almost every fix on these forums with no success but for some reason, these steps fixed it for me. I re-tested this on a friends computer who had the same flicker problem and it worked for him as well. I'm not sure why step 5 is necessary but it appears that using AFR 2 rendering and running the monitor from the second GPU are the key steps for correcting the rendering glitch that causes the flickering.

If you are a Crossfire user and have success with these steps, please post here or PM me so I can update the OP.

Good luck!

Does this also fix the colors in nanovision from flickering? As thats really all that I have an issue with ATM. Some minor other flickers but nanovision is most prevalent.

Does this also fix the colors in nanovision from flickering? As thats really all that I have an issue with ATM. Some minor other flickers but nanovision is most prevalent.

Same here. With all due respect to the OP, my rig is running fine. I refuse to go through gyrations like this in an effort to fix bad programming.

I also have had my hdmi plugged into the lower gpu since the beginning.

Does this also fix the colors in nanovision from flickering? As thats really all that I have an issue with ATM. Some minor other flickers but nanovision is most prevalent.

Yes. My nanovision is now flicker free.

I know you don't want to try all this, so just try plugging your HDMI into your second GPU. I tried disabling AFR 2 and I'm still flicker free. Next chance I get I'll try just changing the HDMI connection and seeing what happens.

I'd love to try, but my gaming PC is out of commission while I await a new motherboard... little ummm incident while re-plumbing my watercooling loop )

Now do you have a fix for 6990 users?

@King have u tried running the game through RadeonPro? Select bioshock as the profile?

Tried this but I have second card in 3rd slot. It's not working for me

Does this only happen with certain cards?.....i've never had any flickering and my monitors are in the top one.

I've got 570 SLI