Not sure I totally understand what is happening, but if the primer is catching on the plate just before it drops into its seating position; make sure that the slot in the collet is opposite of where the primer is entering. Sometimes these will turn just a little and not let the primer drop properly. ???????? check and adjust if that's the case.
Easystreet has the right idea. Raising the handle a little slower and steady will do the trick. With my 366 I can laod almost 2 flats per hr. If all the primers jamb check to see if there is a piece of shot in the hole. Mike K.