It's possible to enable the Simconnect diagnostic mode, this way, to check if there are errors causing pauses:
Open Notepad, and copy the following text:
Save the file as SIMCONNECT.INI in this folder:
Documents And Settings\YOUR LOGIN NAME\Documents\Microsoft Flight Simulator X Files
At the next FSX launch, you should see a text window with diagnostic messages scrolling down, try to identify if there are things that looks like errors when there's a pause.