I have used a D700 almost since they came out and have not had that problem with the flash. The only time it has done anything like that is when it was switched to act as a master for another flashgun and it sent out the trigger flashes but not the main flash, and that is what it should do.
The SB900 is a great gun and I have used three of them for some years with no problems. I think Joseph may have hit the nail on the head when he says you are trying to use rapid fire techniques for far too long. I have used the gun in continuous mode for bursts of eight to ten shots with no problem. How long are you using the gun for without a break? Of course, the ambient temperature will also effect how quickly it cools down, so if you are somewhere very hot it will not cool so quickly. In the frozen UK we do not have that problem - unfortunately!!