Hope you find the problem..........

In a auto loader ball powder will flow a LOT better than any flake or extruded powder will.
One reason I like my single stage, which lets me inspect all cases with a powder charge dropped into them, in a loading tray and a good light source, over head.

You might try Bullseye powder if you have any or a fast Ball powder and see if the problem stops.

A loose fitting bullet will fire but it will probably not group with the other bullets due to loss of fps if at 25 yards or more.
With a tight die, your bullets should be all loose or all tight, unless you have poor bullet dia. quality.

I will put money on either powder "Bridging" or primer hole obstruction as the culprit.

Primer hole problems are a sign of improper loading steps taken. Correct this, before you go to priming the case.