Ok, I re-read the OP's post. Does the primer arm swing in and out of the ram as you raise and lower the ram? The primer arm could be binding in its slot so that it remains in the upright position.
I assume you are able to deprime and insert a fresh primer. You can still do this with a primer arm stuck in the vertical, in which case, as you de-prime, the spent primer then falls on the primer arm and out the ram's slot.
Make sure the primer arm is free to swing in and out of the slot. When the ram is at the bottom of its stroke (operating handle is at the top), the primer cup should be inside the ram in order to seat a new primer. As you raise the ram, the primer arm will swing out, so you can easily insert a fresh primer onto the primer cup. At the top of the ram's stroke (the operating handle is at the bottom of its stroke), the old primer will be pushed out and fall into the hole in the center of the ram, into the clear plastic tube at the bottom of the ram.
As you lower the ram, the primer cup will be cammed into the vertical position to seat the primer.