You are aware that there are 2 sizes of primers and that there are 2 different cups to use, yes? (primer not centered in cup suggests small primer in a large primer cup. Small primers in large primer feed tube would cause droppage.
Too tight on the bolts holding the primer feeder can impede shuttle movement. They don't need to be very tight. (finger tight plus a tiny bit)
There is some slop available to adjust the primer feeders position on the press. It straddles the shuttle so it might need to be aligned better.
Upside down primers come from- handling pickup tube roughly, wrong pickup tube, wrong cup, or jerky shuttle movement.
Jerky movement from roughness or debris under the slide. This area should be smooth and free of oil or lubricants. Yanking the operating handle up and down too quickly can also cause problems.
(I've loaded over 20k rounds on my 550b. Very few setup issues but the operator has to learn how to set it right and operate it right.)