Well, if it were the cases alone that would explain it. I was able to dissassemble two cases that wouldn't chamber and remanufacture them so that they would. I think it may be cause by the bullet seating and/or the cases used.
I added one check to my loaded .45acp and that is a chamber check. I removed the barrel from my colt and used it to check each new round before I put it in a box. I found two that wouldn't chamber and remanufactured them. They worked fine after that.
The cause I think may be the seating die itself or the amount of "belling" the case gets from the charging die.
Still not sure the cause but the chamber check seems to shake out the few cases with a problem.