My friends AR was doing the same thing when new. Certain ammo would cycle fine but some would not. We checked everything including the mags. Finally spoke to an retired armorer and his comment was just to shoot it more to loosen it up. Guess what..after running a few hundred rounds through it, it now cycles fine.
Try inserting the mags with the bolt retracted to make sure they seat properly and see if it continues to short cycle. Also shoot good quality factory ammo if you don't reload.
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