I had a similar reject rate on first batch of .40 cal in new 550. My problem turned out to be a combination of two rather simple avoidable set up errors. Unlike you, I did not set the Dillon resizing die correctly. That left a very slight bulge in the case at the rim. Measured at just above the extraction groove, cases at 0.429 " wedged, cases at 0.424 plunk nicely into my 96A1 barrel. I am used to making my mistakes in a single stage press. Can't crank out much of a mess doing it one at a time. The Dillon is a different story. I learned.
The other mistake I made was to put too much crimp into a Rainier 180 gr RNFP Cu plated bullet. That bulged as well - just at the other end of the round.
In both instances, my mistakes caused the problems. Detailed measurements and dropping set up rounds in the barrel resolved the issues. Since correction- the Dillon has cranked out 600 perfect rounds.
One other note, my practice is to push all range brass through a Lee Bulge Buster before they join my notably random mix of brass. Perhaps not necessary, but it does take one more variable out of the equation.
I hope this helps- at the very least, now you know you are not alone.
