Many good answers here!
The range I formerly worked for (mid 80'd-mid 90's) loaded well over a million rounds a year as "range ammo", from harvested cases and lead. I can tell you with absolute certainty that the 9mm case gave us the most trouble out of any cartridge.
The cause of the problem was two-fold. First, 9mm chambers, and more specifically the ramps or unsupported part of the chamber, varies all over the place between all the manufacturers and even different models from the same company. Second, being slightly tapered, when sized, the 9mm case tends to "flow" brass toward the head of the case. That second problem tends to be an issue when cases are resized several times - as you may be encountering, and as we certainly encountered recycling all the brass we would sweep up each day.
The result is that 9mm cases get a bit of a fat ring of brass, or bulge of brass that may go around the entire case close to the head, or just be a bulge where a particularly unsupported section was located.
Our "fix" was also two-fold. First I modified the sizing die with a diamond wheel on the surface grinder. I think it was close to .020 that was removed from the length, which had the effect of reducing the diameter of the carbide ring's entrance. The die was then seated lower. That took a bit of trial and error, because the 9mm's were loaded on a Star progressive machine and I didn't want to have misalignment issues - some bell, or flare in the die was necessary.
The next thing I did was reduce the thickness of the shell plate, which had the effect of shoving the case into the shortened die a bit further. I think in total there was about .030 more insertion (give or take) all together.
That cured about 90 percent of the "fat 9's". We had a "dud" box, and when a shooter would say a round wouldn't chamber, we'd just toss it in the box. When bullet pullin' time came around, the 9's got tossed for scrap, not worth pulling. And by the way, one of the guys had a really nice puller he invented. It was two plates, with holes like chambers on a revolver. The lower plate was cut for rimmed cartridge heads, the upper plate had access holes for the lower plate, but twisted on three slots held by bolts. You'd load the plate, twist the upper to keep things in place, then put an inpact hammer in the middle from the bullet side. Press the whole s'bang against an old tire we had for that purpose, and hit the trigger on the hammer. Six bullets would pop out in the blink of an eye. Made bullet pulling for 45 colt and 44mag/spec... 38/357 really fast n easy. Most of the time we had a bad primer, or reverse primer, that sort of thing. I think we set someone to pulling bullets... about once a year, when the box looked like it was getting too heavy to lift
We didn't have that many duds.