Also, are you running ISBoxer?
no

What core affinity is set for the two instances?
Didn't make a difference when I set specific core affinities.

Does adjusting the in-game settings make a difference?
Setting it on High increased the frame rates to ~15 fps, but it was still very choppy to play

Do you have any other "blended" graphics objects overlaying the game? (ATI hates this in my experience)
No

+1 to disabling crossfire. Unfortunately, sli and crossfire do not seem to work well with WoW, especially when in windowed mode.
did that. it did help slightly, but still crappy.

Also, I know it may seem crazy, but also make sure your system power setting is on HIGH PERFORMANCE.
it was on that already.

Atm, if one of my character is in Org and the other one is somewhere else, the org character would get about 15 choppy frames while the other one would be about 30.