You answered your own question. It's the cases.
They're not all created equal !!
Identify the case head stamps that are giving the problem.
My guess is that they will either be Military or the "odd" forigen manufactured brass. Sort the brass by head stamp and trade out or throw out the out-of-spec brass. I find that Federal and Winchester .45acp brass is the most consistent, with Rem-UMC head stamp subject to some really thick ones-(And thin ones too!).
"There is no such thing as a second place winner in a gunfight" Bill Jordan