I have had this problem since release and have tried several things to try and get around this but for me with SLI on and ultra or even high settings i get stuttering and single digit frames in some ship areas. With SLI disabled the fluctuation is not there even on ultra. Now i poked around in the Varibles.txt (My Documents/StarCraft II/Varibles.txt) and for a random reason I decided to change shadowmapsize=2048 to 1024. Now granted with SLI off 1 8800 GT handles the ship areas fine, why changing shadows to a lower resolutions helps with SLI on I'm not sure. But I have tested it several times and with this i get ZERO interruptions or slow downs in any ship areas on ultra settings + SLI.
Would be nice if someone could test this and see if its not just my rig.
GPU memory usage seems to be the same. Not enough to say i was overloading the cards memory, and if i was why would disabling SLI then cause it to stop stuttering if i was still maxing 512?