Just had this same problem. The shell plate was not rotating all the way to center. The primer was being seated to one side of the primer pocket causing it to flip sideways. Mine was caused by the wrong locater pins, #2 instead of #3. This caused just enough drag on the casings to misalign the shell plate.
Check to make sure that you don't have the shell plate or primer plate too tight. A good cleaning and greasing may help as well.