BRAVO1NINER -
I have had a similar problem, a few years ago. IIRC, it involved a Ruger #1 in .30-06 and a SA Garand with a "match chamber". Brass fired in the Ruger #1 would not fit the case gauge, even though the gauge is made deliberately oversized (in dimensions other than case head to shoulder datum) to permit measuring fired cases. After resizing, it would fit, but then it would not chamber in the Garand. It did chamber in the Ruger #1.
I had the Ruger #1 rebarreled before I could determine whether it was excessive headspace or an oversized chamber. Measurements of the case showed the diameter just above the head was not being resized enough to suit the Garand.
Cases fired in the Garand resized correctly.
Perhaps a small base die would have made the brass fit, but if I continued to "mix up" the brass use between the two rifles, I would eventually experience case head separation due to overworking the brass, I presumed.
With a Pac-Nor barrel on the Ruger #1, it is now close enough to my other .30-06's that I don't have to segregate brass. I realize segregation is a tool, and I do use it. I just didn't want to
have to do it.
So, with all the variables involved in resizing brass (including mfgrs variations in case wall thickness, lube variation, chamber dimensions, and how many times the case has been reloaded), it is quite possible to have cases that don't size the way you want them to. You can even have trouble getting them to behave with the same exact setup, due to increased "spring back" as the case work-hardens.
Also, in describing the dimensions of a case gauge, I am referring to the Wilson type, which is quite common. All case gauges are not Wilson type gauges.
I have read of reloaders making their own case gauges with a suitable barrel section and a chamber reamer. These are definitely more of a chamber substitute than the Wilson gauge, but it is hard to say how useful they are for a particular rifle.
Back to your problem. If you are having some cases drop in to the chamber, and others don't, that indicates that you are experiencing variation in resizing. There is some difference happening. Try to figure out what it is.
Are the oversized ones all the same headstamp? Were they all fired the same number of times? Is your lube application method consistent? Are you holding the press handle down the same amount of time?
I'm still learning about this stuff, so I'm not trying to position myself as an expert. I fought the same stuff just a few years ago..