I asked someone whose been out of the military for a while now and he said that the GPS they use is completely different from the GPS you and I use. They have their own separate set of satellites, different frequency, etc that has replaced the system we use. He couldn't give many more details since that was classified.
The US military uses standard GPS. They used to use Selective Availability to encrypt part of the signal to reduce civilian GPS precision, but that's been discontinued.