Yet another variable:

Some cases fit the shellholder as they should, with the flat part of the case resting against the flat part of the shellholder. These maintain their concentricity throughout the cycle of neck sizing.

Others rest against the 45 degree cut on the case extractor groove and the coresponding 45 degree cut in the shellholder, rocking back and forth. These are not concentric after sizing.

Hmm...

I chuck up my pistol shellholders in the lathe and cut about half of the top off. It allows the carbide ring to get farther down the side of the case and also I expect eliminates most of the wobble problem. Personally I've never seen the issue you describe, but I don't load all that many different calibers. What caliber and shellholder brand are you using?

I used .22-250 Remington brass and RCBS shellholders. The bad ones had .002-.003" runout at the neck after partial neck sizing. The good ones were all under .001"