Have to ask this, does the game hang on loading screens? Happens to me sometimes.
Edit: Gonna expand a bit, everytime I go through the Whiterun gates, it would hang and load indefinitely, I looked around the net a few days ago for a fix, and someone said that if you unpack the Skyrim - Meshes.bsa it should fix it, I was skeptical ofcourse, but I went and DLed FOMM and unpacked the entire Meshes.bsa into a folder on the desktop (not even putting the unpacked meshes into the data folder), restarted Skyrim, worked like a charm and has since. Hope this helps you pal.
Side note: Anyone have any clue whatsoever how the above process worked? I was gobsmacked (but delighted) when it loaded me into Whiterun. (Had made a QuickSave at the entrance, to check a mod wasn't doing it, removed all mods, still happened, then I went on my search for the above, and it fixed. I don't question it, it worked after all, but I don't understand it, that makes me sad.)