I built a new system and was playing some Skyrim to check things out. I was getting pretty insane FPS but it wasn't really registering with me. With an I5 3570k and an HD6950 I was getting way above 100FPS with settings detected at Ultra. I hadn't turned vsync off so it should have been capped at 60. I just thought it was something with the video driver and not initiating vsync. I used an FPS capper to stop the physics issues and thought everything was ok. None of the ini settings were changed from default, the iPresentInterval was still set to 1.

I installed the SKSE so I could run SkyUI, and I noticed an instant drop in FPS to the 40s (which is about where my system should be when at max graphics) and this made me take a good look at the game. After doing some comparisons it was easy to see that just a couple settings weren't being applied when running the game right through Steam. No AA or AF, no vsync, I could feel the mouse acceleration kicking in when it wasn't before. Renaming the ini files in My Docs and having the game create new ones didn't solve the issue.

Chances are I won't be turning off SkyUI so I'll always be running the game through SKSE, but if I do play without SKSE these issues are going to come back. Has anyone else had their game just ignore certain ini settings? What should I do to try and fix it? I don't have Dawnguard yet so I don't know if installing that will change things or not. I'm running Lucid VirtuMVP so I don't know if that might be screwing with things or not.

Is your game a straight Steam install or is it a disk install into the Program Files directory? If it's in Program Files, try installing it into it's own directory, ie C:\Skyrim.