If the mission involves a carrier and a defensive fleet around it firing at maximum firing capability (its possible in the mission builder to set how often ships will fire) then thats enough physics calculations to bring any CPU to their knees. At this point your graphics card is waiting around for the CPU to complete calculations...so the FPS drops.
Run the track called 'blackdeath.ntrk' and record the FPS start the finish. Write down the lows, average, and high. Let us know.
You have a slightly older CPU paired with a very fast graphics card. You're likely CPU constrained.
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