I'm not sure of how this will go over, but I reccomend turning off transparent windows untill performance is improoved. I noticed two things: First, if you turn off your GUI, the frame rate is much much better. Second, if you overlap two transparent windows, your frame rate drops dramatically. What this is telling me is that the GUI color mixing code is poorly done, and I think we would see a big frame rate improovement in the game if it was turned off untill EI can improove it's efficiantcy. I don't have any real proof that it's the transparency alone, but I have a very strong huntch.
Hmm.. on a side note, I wonder if there is an option in the settings to turn off transparent windows... I will have to check later.