First check the cases that experienced the tipped primer, is it a military case? If so is there adequate chamfer in the primer pocket? Holding the tool at significantly less or more than 45 degrees from horizontal can cause the primers to tip.
If you are significantly less than 45 degrees the primer will not slide completely and briskly onto the pin you then have a condition where the primer is half on the pin and half off. A tip is likely to occur. Significantly steeper than 45 and primer slams into the end of the channel and tips upward into the open primer pocket. With this bit of information your problems will likely disappear, if not try cycling tool without cases. Lift the primer off the pin on each dry cycle. If they aren't 100 % upright you should quickly see the problem if you see something wrong please let us know.
