Simulation Restarts

So I plan a trip via PPFX.  Export the flightplan to FSX-SE.   Set up my aircraft and departing and destination airports with Aerosoft Simstarter. Get it all started, with Active Sky loaded and the sim looks good to go.  Then I notice that the simulation is choppy and the FPS isn't what it should be with my FSX config settings.   I close out everything, reboot the computer and reload everything.  Then it purrs like a kitten and the simulation runs smooth and sharp.   

Any ideas on what causes this?   I have a strong computer.

Thanks in advance.