Thanks again for all of your thoughts. Since the problem seemed to be with the camera firing, I had not been focused on the flash as the possible cause. But it does make sense. I had forgotten about the shut down feature of the SB 900, and also it sounds like it overheats faster since it's more powerful. So I'll now pay attention to that more closely. I did update the firmware on both my cameras yesterday, even though they were up to date, just in case there was a corruption as you mentioned Gary. I do also use a battery pack and Eneloop batteries as well, but I will look into turning off the thermal protection, thanks John. And while I don't think contacts are the issue in this instance since I've had them replaced, I think it is a good idea to add CRC QD Contact Cleaner to my routine Myer.
In Rob Galbraith's review of the SB 700 vs 900, he mentions powergenix nizn 2500 batteries, which I've never heard of. He says the recycle time is about a third of the Eneloops. Would those be better than the Eneloops? It's a bit confusing because he talks about the fact that lowering the recycle time actually leads to the flash overheating sooner, so it's not clear which is the better direction on batteries. http://robgalbraith.com/bins/content_page.asp?cid=7-10058-11116