Actually, polar bear, now that I recheck, my results mirror yours (1-->2).

SLI: my results
1x 8800GTX: 13003
2x 8800GTX - SingleGPU mode: 12892
2x 8800GTX - AFR1: 9888
2x 8800GTX - AFR2: 15594

Driver: 169.21
Vid BIOS:
#1 - 60.80.0e.00.05
#2 - 60.80.06.00.12

You put yours on AFR2? If you left it on default, switching to AFR2 may be the trick for your system - because I would think you'd get at least a couple thousand points above my score, just based on your OC.