It sounds like the problem could be occurring when the primer feeds from the magazine tube into the primer holder on the slide. Try taking the magazine tube out of the blast shield, cleaning it, and making sure that it is properly positioned into the block when you put the cap on the blast tube. Don't put any pressure on the magazine tube when you tighten the cap down.

Make sure the primer holder on the primer slide is clean.

If you are using the plastic follower in the magazine tube consider adding a little weight (45acp case) to it to make sure it can press all of the primers down.