For a while now Sins has been known to randomly speed its self up when playing in a multiplay game not hosted on ICO. Play any LAN game and it randomly runs at 2-3x speed, then slows back down to 1. Even autosave timing is affected by this.
I had a theory that the host was outrunning its self and sped up to catch up to its self, but someone said that can't be the problem. However, since 1.1, I have now noticed this happens in single player, too!
Using Medium-large random with five hard AI and one human, I have noticed that the game will progress at normal speed for one second, then speed up to about 1.5 speed for about .75 seconds before slowing down again. This is especially noticeable when you zoom in to watch a battle up close and look at something slow moving, like a phase missile.
The UI in Sins does not lag when the physics are slow due to a massive amount of units. This leads me to believe that Sins is using two threads -- One for gameplay, containing all the ships, weapons and what-not, and one for the UI. I believe it is due to some timing synchronization issue between these two threads that the game randomly changes speed. If I had to wager a more detailed guess, I'd say the UI thread is running ahead of the gameplay thread (purposely), but it's going just a /liiiiittle/ too fast and the game keeps deciding to play catch-up, which makes the UI thread go faster. Just as the UI thread goes faster, the game thread thinks it's caught up and slows back down again, but now that the UI thread is going faster Sins gets back into the same situation it was in before. The timing between each thread checking on the other is /just/ perfect so that it doesn't create an endless loop of increasing speed, but rather a fast-slow pattern.
I hope this helps someone track down exactly what's causing the issue. It's been here since I started playing Trinity and it's always driven me nuts.