It's hard to say.
1. What version number of the game are you in? A lot of improvements have been made recently.
2. Are you in a huge battle at the time? Thousands of ships vs thousands of ships? If so, it might just be a ton of calculations.
3. You can try going into the Stats section in the game and adjusting the simulation speed from there. The game actually only changes the updates of the game at whatever speed is set there, so even if you have a higher FPS it is not drawing game updates any faster (just things like hud movement, scrolling, zooming, etc.
Hope that helps!