Usually it is the last round that fails to extract, bolt locks back but the round is still in the chamber. Sometimes hand cycling works, sometimes it take several tries for it to strip the casing out of the chamber.Just to be clear on your problem:
You fire, the empty case stays in the chamber, the bolt picks up a live round from the magazine, and attempts to feed it into the back of the empty case?
The upper is a Gibbz side charging, bcg is an unmarked dpms pattern, has a 18” Faxon pencil barrel with the superlative arms bleed off gas system.I'm curious OP. What brand upper and bcg are you using?
Barrel also?