I and my friends have noticed a problem that was mostly gone in the previous beta that's returned in the current.
We play multiple AIs cooperatively pretty often. The problem happens near midgame when the entire game slows down drastically to the point of being almost unplayable. I check the CPU load via the in-game meter and nobody is over 50%.
I'm always the host (using the traditional port forward method) and watch my own CPU usage through a sidebar applet and again, never above 50% usage.
I can even experience it locally during a replay once the game gets to the same point, but again I'm not seeing the CPU usage top out, nor is the hard drive thrashing around indicative of memory issues (granted I've got 2GB).
A zip file of all recent gameplays (some may not have it but to be honest I don't have the patience to watch all the replays to see if they do or not...as a side suggestion add a seek bar to replays PLEASE). They can be found at:
http://bonerax.com/SINS/mprecords.zip
We'll be happy to help in any way possible to help zero in on the problem.