Strangely enough, I loaded some .45 last night, and in 50 rounds I had 11 primers go in the case sideways with my XL650. Never had a problem before.
I played with it a bit and found that there was a film of goo between the shell plate and the ram platform that was impeding the full rotation of the shell plate. With the goo in there the detente ball wasn't fully engaging the shell plate, so the primer pocket was not properly aligned with the primer punch.
Cleaned it all up and the shell plate snaps into position and the primers all go into the cases nicely again.
There was very little goo, but just enough to cause a problem.