Solved. Found out that the Unofficial Skyrim Patch caused my problem. Really strange. Tried to only have the DLCs active + Alternate Start, worked fine, tried with the highresdlcs + Alternate start, worked fine. Tried with the unofficial patches (except dragonborn) + Alternate start, didn't work. Tried only with Skyrim unofficial patch (of the unofficial patches) + alternate start, didn't work. Tried with all the above except dragonborn patch and skyrim patch. Worked fine. It's either that the latest unofficial skyrim patch bugged out, or most plausible that it bugs out with the latest version of Alternate start. EDIT: Updated with the unofficial DB patch and the skyrim patch + everything else. Worked.