I believe I can see the burr that butlersrangers is talking about at the junction of the extractor groove and the chamber mouth. Does it make a mark on the front side of the cartridge rim?
FredC, why would the barrel need to be removed to lap the bolt in?
Also, as open as the Krag is, could not a small inspection mirror be used to look at the receiver bolt lug seat? That could be informative.