Drew, the case is inserted all the way into the shell plate at station one when the primer is being seated. If you are occasionally getting a case that isn't all the way into the shellplate, and thus isn't lined up with the sizing die, there are only two things that can cause that. You either:
1) Aren't completing the full range of motion when priming, either because you simply aren't, or because something is in the way and blocking that action (like a spent primer that wasn't deprimed at station 1), or
2) You are fully pressing that case into the shellplate while priming, then it's sliding back out when you start the ram back up, which seems incredibly unlikely.
Far more likely you're not rocking the lever forward all the way on priming.
You're not the guy who recently said he was depriming and priming separately from the progressive, are you?