By chamber check, do you mean check it with headspace gauges? Sure. But your case comparator should give you some idea of that. Compare a new case with your extracted case. The new ones are usually around 0.002" short of minimum chamber length in .308, but putting the comparator on a headspace gauge to check the difference is your best bet.
To your long brass problem: First, be sure the die is adjusted correctly. For full length resizing, you want die contact with the shell holder when a lubed case is pushed fully up inside the die, and not just without the added resistance of the case pushing up on it. It's little hard to see a crack of light between the die and shell holder on the Co-ax, but a 0.001" automotive feeler gauge can be pushed around the edges of the die to verify it can't slide in to touch the case.
Take the cases that are staying too long and put Magic Marker on the heads of a couple of them and rub them against something flat, like your bench top. That will reveal high spots. Self-loaders commonly bend rims out and that messes up the resizing process and, even when fully resized, can still prevent chambering. The bent rim may tuck under the Co-ax shell holder enough to preserve its bend, so the whole case comes out long. I've not verified that, but imagine it may be possible.
Usually you can spot bent rims because the cases don't stand quite straight on a flat surface. They won't drop in your Wilson gauge, either. The rim will hang it up, and, again, a little Magic Marker will show you where it rubs.
The bent rims will flatten out when firing, but first you've got to get them to fit in the gun. One technique is to get the $16 adapter Forster makes for the Co-ax press that lets you use it with standard shell holders. Collect the tall cases and sepearate them. When you're ready to fix them, take the decapper out of the die and put a feeler gauge into the holder under the case rim. That will let the sizing die set the shoulder back further by the amount of the thickness of the gauge.
If there isn't a bent rim, the possibility mentioned earlier of the expander pulling the necks out or at least off-axis of the sizing die is also real. That's easy to test. Pull the expander/decapper out of the die and resize without it. If the cases then all come out the same, put the expander/decapper back, but just run the case in far enough so the mouth goes over the expander, then back it out. You'll have to decap with a separate Lee Universal decapping die, then, but that's a quick operation. I think the Dillon dies all use carbide expanders, so inside neck lube shouldn't be required, but you can try a little graphite powder anyway.
Have you checked with the case headspace comparator after the cases came out of the LR but before you resized them? If hard extraction is the problem, the trouble makers should show up then.
Oh, one more thing: bent rims usually favor one side. Have you tried rotating the long cases in the comparator? If bent, that will normally cause the reading to change as you go around the clock.
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