On top of this, the console isn't working. The command to set the quest stage doesn't work. It'll go through on the console screen, not saying that it didn't recognize something, but it will have no effect whatsoever.
When the problem first started I had a ton of mods on, but I've since reverted to old saves, unninstalled all mods, and reinstalled Skyrim. It really don't think it's caused by mods.
Oh, and might as well mention it that the Vigilant guy at the start of Dawnguard is somehow alive when I get to Dimhollow Cript, even though the vampires there are talking about how good of a fight he put up though he didn't have a chance.