I'll occasionally check my SkyrimPrefs.ini, and I keep noticing that iPresentInterval is getting reset to 0. I assume this still disables vsync and thus causes all kinds of bugs. Any idea what could be making this happen?

Check the ini files in the Skyrim root directory and make sure none of those have been modified to have iPresentInterval = 0.

It works kind of the same as Unreal3 Engine ini files, where you have default values stored in the game's directories, and user modified ini files in the %user/documents folder.