I'm having the same issue since the update. Its not an issue with settings or my updates (I presume) because 1 in 3 times...same right click "open as layers" it will work. 2/3 times or more it will open with the first image in the series as a "background" layer in another document. ALSO, if I drag and drop that "background layer to the other layers the auto align will not align the image (as if it was taken with a different lens or perspective). However when they do happen to open together as layers, they all align fine!
This is getting VERY frustrating - exposure blending is the bulk of my work and since this update my editing time has at least doubled due to these types of glitches Gerrrr Adobe.