Much has been discussed regarding the Thermal shut off switch in the SB900′s. There are many things that contribute to this. First is using the dome on the flash at low ISO’s. This causes the flash to dump at full output, requiring the flash to recycle the capacitors back to 100% from 0. If you are using rechargeable batteries with a mah rating of 2650 and higher, those batteries are going to contribute to the unit heating up. Also, shooting outside while it is above 80 degrees will also contribute to the unit overheating.
What to do? first, use the dome when you can bounce off of a ceiling of 12 feet or less. Second, try to use an ISO of 800 or higher for rapid shooting if the ambient light permits. Third, keep the aperture between F5.6-F8.0 if the ambient light and depth of field permit, and fourth, try using 2000mah batteries instead. The lower mah will not heat up as fast and will keep the flash from going into thermal overload. There are other things that may help keep this at bay, but this should give you a start. Also, Sanyo makes a Hybrid battery (Eneloop) that can hold 85% of it’s charge after a year in storage.
Happy shooting!