Are there a lot of dynamic entities in the areas where you slow down? (Are there a lot of entities period?) There are probably many factors coming into play, and there is no single solution. Optimization is key. Are your textures all 4096x4096? If they are, you might try dividetexturesize=2 in your setup.ini file, or reducing your texture sizes manually, which of course, you would save the originals elsewhere. Animated entities (like most of the trees) are frame rate killers as well. Shadows, water, terrain, physics, blah, blah, blah affect things too. Use f11 and f9 and you may get an idea of where your troubles are coming from.
EDIT: LOL, I just re-read your original post, after reading all the others I forgot you had used f11. The rest still apply, though!
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