I put the 70-200mm IS lens on my Canon 40D and tried the same thing and all worked fine. Flashes were not attached to either camera as I wanted to check the low light focusing capabilities of both cameras without focus assist. I had much better luck with the Canon.
Anyway, back to the Nikon manual to see if I'm missing something here. If anyone has any suggestions for Nikon camera settings for optimum results in low light focusing situations, please let me know.