As mentioned above Clear Sky has always been the most problematic. Try messing with the Sun Ray settings if you haven't already, I'm sure I read somewhere before, possibly a mod that the engine in Clear Sky still tries to render them from the light source even when they aren't visible, thus giving you a performance hit for no reason. This might all be complete nonsense but it always seemed to work for me. Sun Rays don't even effect performance for me in COP, even heavily modded, just Clear Sky for some reason.
It might also be all the AI straining the performance, I remember there being a lot going on at times in the background, far more than the other games. That first area in the swamp calms down after a little while so it could just be that. The actual base itself tends to give bad performance anyway, lots of shadows, light sources and crazy amounts of sun rays get thrown in there at times.