It sounds to me like the extractor notch is either not properly aligned (so as to be wide enough) or not properly angled to allow clearance of the 'claw', when it is holding a cartridge by the rim.

If both of your 'bare' Bolts will close on a cartridge, the Notch is the problem.
(Note - The sides of the barrel notch have to line up with the notch machined into the action and not make it narrower).

Clear photos of your barrel breech may allow us to spot something.

Attached photos to see one that works:

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