I had a similar problem, except it would happen ALL the time, instead of just once in a while.
Are you holding down a key when the frame rate drops? If that's it, then check for weird applications that might be running, using ctrl-alt-del. I had something called Kernel.dlI running... it would use up all the processor power on a 1.4 GhZ AMD, just for pressing a key.
It also might just be that someone decides to get into the carrier, or the AC-130 (in desert combat). That'll slow anyone's game right down.
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