I just can NOT get the Lee full length sizing/decap die to be consistent against a 9mm case checker. 2 or 3 will be flush. 2 or 3 will be a bit high.
I would check to see if it’s the rim, that is the issue.
I tried it all from turn down until it just touches the plate and then tightens the ring to give it one quarter turn after it touches the plate to give it a half turn after it touches the plate and tighten down. Tossing out brass that doesn't fit fresh off the press wouldn't be economical because that would be maybe 1/3 to a half. I'm beginning to wonder if perhaps I just got a bad carbide sizing die and should buy a new one.
Unless you can crank your size die to below the shell holder, you can’t fix the rim with it, obviously that part is still in the shell plate to pull the case back out of the die, so it can’t be sized. Run a case all the way up into the size die, the part you can still see isn’t being sized.
So, the first thing I would check is if the rim base are In spec. I do not do this with my aluminum EGW case gauges but use my stainless steel ones.
If the round doesn’t drop in and out of the gauge, put it in backwards and give it a twist.
If it’s good now, that was your problem.
Plunking won’t do you any good because it would be abnormal for the rim to contact any portion of the barrel.
So what you wind up with are mystery malfunctions because they all plunked fine but the problem finally showed up when it comes in contact with something that will stop it, like the breechface/extractor.
There are machines out there for sizing the portion of the case the normal process doesn’t touch. Roll sizers can even get into the extractor groove.
or you can push them through a die that will ensure that at least the OD is good at the base.