After I updated Skyrim from version 1.2 to 1.5 it stopped using the normal ini files (Skyrim.ini and SkyrimPrefs.ini) and Saves-folder located in C:User name\Documents\My Games\ Skyrim. This caused all sorts of weird effects, e.g. the game starts in a small window, there's no music in the main menu and the framerate has decreased considerably. The patch works perfectly with my other computer so I know this problem has something to do with this computer being improperly configured. I've already tried reinstalling both Steam and Skyrim, running as administrator and using the newest graphics card drivers, but none of these fixes helped. I'd like to hear if someone else has already encountered this problem and possibly fixed it.

EDIT: I have the same problem as this guy: http://forums.nexusmods.com/index.php?/topic/480168-my-gamesskyrimskyrimprefsini-doesnt-have-any-effect/
The music in the main menu is actually playing just fine but the other issues still persist.