I've run into this problem if I set AA mode to Adaptive.
LiquidMetal14: Have you tried SSAA as well? It's what I've been using and the FPS hit compared to Adaptive is not bad on my system (2x6950), plus it seems to play a bit more nicely with Skyrim and you don't have to deal with puffy transparencies.
BTW: Have you considered linking people to Notepad++ in the OP? Considering how much time people will be spending in their .ini files, a more organized text reader may make Skyrim tweaking a less daunting/tiresome experience.