Seems that way. If you look at how it recorded my specs: GPU clock=413MHz (about half) Vram=24MHz (umm...).
I actually made two runs and I think I can determine that for all the encoding and HDD tests that you will receive a higher score by running a strap that has the lower latencies. My score I posted above was running a single 3870, 3GHz core on the 1066 strap, which is good for MCH speeds. My second run, I enabled CF and ran the CPU @ 3.75GHz on the 1333 strap, which you lose some performance until you reach about 500 FSB (which my board cannot do!).
So right there is a tip to help boost your scores in this bench.