FWIW, I shoot off the bench using the cheapest mags known-Thermolds. Price doesn't always assure functionality. I've never seen commercial .223 ammo that failed to function an AR(that doesn't have problems).
It's quite possible you have some drag on the top round in the mag during feeding. My common test for full bolt travel is to fire one round and see if the bolt locks open-just as the OP did. Three such tests w/o a miss has been good enough for me.
I'm assuming your gas tube is dead center and the gas key slides over it on return w/o any snags. Since you commented about the PITA freefloat handguard, I'd check to make sure the gas tube to key fit isn't part of the problem.