I have had the same, but I have not tried it with the refresh patch yet. I think its because of the battles that are taking place. Play as galcom, and try to get in to a big battle (maybe take on a starbase or something). I noticed it only did it when carriers or cruisers were around, but then again, I gave up as soon as it slowed down, due to its unplayablity when it did. I havent properly tried out the refresh patch yet, but the previous 2.09 did this with me. Try it, see what happends, take note of things like.. are you in a battle, or is a battle occuring in another area.