I had similar issues with the last beta patch. I am running dual 6970s on 3 monitors, and would sometimes get blazing performance (60 to 90 fps at 5176x1050) on mostly high settings. I could fly the same mission immediately after and it would be running in the mid 20s to mid 30s at best. I could find no pattern, sometimes it worked great, other times only barely playable.
The good news is, with the current official patch,it is finally consistent... it always runs poorly.