dino... let us know what he tells you. Sorry about the problem. Hopefully he'll straighten it out for you.
since the Lapua cases are doing the same thing... I have a thought that you might share with the 'smith, for him to check out. Be sure to take some fired cases to the 'smith as well.
If your scope base screw is too long in the chamber area, it's pressing against the bolt *slightly*... and this would mis-align the bolt just slightly... with new brass (smaller base) the bolt can "duck" under the long screw (we're talking a thousandth of an inch of clearance or so, the tolerance is there...)... With fired cases, the bolt is held up against the screw, higher, with no wiggle room at all.
By turning the case (re-indexing it), and re-inserting it, you're not lining up it's egg shape with an egg shaped chamber, but you're simply finding an extra thousandth of clearance, just by happenstance, either on the bolt lug or in the fit of the case head to the bolt (the rims are not perfect circles, they'll be out a thousandth or two one way or the other)...
If your chamber was egg shaped you'd see rub marks on opposing sides of the case, but you're seeing them only on one side, as if the brass is being held off axis
with the chamber... a bolt that was being pushed down by a base screw that was too long might do this.
Of course you might get told any number of things by the 'smith, and depending on his credibility they may or may not be true. Hopefully he's a straight shooter.
If you haven't shipped the rifle yet maybe you should remove the scope base screw over the bolt lug area and see if it's gnarled up on the end, and see if there might be a corresponding wear mark on the bolt in that area...
Just a thought.