Nvidia sli or ATI crossfire (i think thats what its called) is not supported in FFXI and I've heard of some wild issues coming up when it's active.

Other then that, FFXI is special in the way that it runs. Unfortunately, comparing this game running to any modern game on the same rig just doesn't apply. FFXI was never really supposed to run in windowed mode to begin with. They gave in and added it in a patch some time after release. From quite a bit of the feedback that I've seen it was just thrown together at that.

The best answer I can give is to make sure your drivers are updated to a least the 314 version ( I think that one had a note about ffxi on newer cards as well). I'm running the newer 320 ones and don't have any issues atm.

I've never used sli, but I hear disabling it completely while running ffxi helps.
There is a check box in ffxi config as well called Graphics Stabilization that is supposed to fix certain issues as well.

Sorry its not the best answer, but hopefully it helps at least a little.