When your bolt close on a hand fed round the extractor HAS to ride up over the rim. Not sure if one coming in from the side has to ride as high to get over the rim.

There is a recess in the receiver that lines up with the recess in the barrel. Check that and see if it is full of hardened crud. Maybe it is limiting the ability of the extractor to lift over the rims sometimes.

Krag bolts sometimes get some wear in the center of the face. A go gauge with no bevel may have the outside of the rim touch the portion of the bolt face with no wear. If the end of the barrel and the bolt face are both clean, the go gauge should go any way as it did when everything was nice and fresh. If we do not get your problem ironed out soon you could send me the gauge for measurement. I would have thought a gauge with the wrong thickness of the head would be extremely unlikely but your are second in a the last couple of months with the issue. Maybe a handful of gauges escaped final inspection.

Before we go too far do your new unscarred rounds chamber easily with your "naked" bolt ? How about the scarred rounds? New magazine cut offs are relatively cheap, a modified nail maybe needed with your sight.