Hmm, a tricky-to-reproduce one, eh... and 10 minutes in the game should be pretty well done with recalcs, most image loads, etc.
Doing my normal "pin the tail on the donkey" method (run it in the debugger, periodically pause it, and see what line it's on, and do that several times to see if it happens a lot in the same place) I wasn't able to find anything particularly notable performance wise. Lots of time in the move function, lots of time in the collision-check function, nothing much new.
However, I looked around a bit and found that on the Icul planet (the devourer one) there's also, oh, 7000+ minor-faction resistance ships. A bit further in it jumped to 14k+. Given the O(n^2) cost of collision checking all ships on a planet (among other things), I've got my suspicions about the cause of the slowdown.
Apparently they're launching a raid on your framerate.
Is anyone else seeing an improbably large number of resistance fighters showing up?