Humm, different bolt, same problem. How is the rim on the spent casings? Are they chewed up? Take a spent case and drop it into the breach. Release the bolt. Can you pull back on the charging handle easily to extract the case or next time at the range, with the rifle pointing downrange, insert a mag into your rifle with a round in it, release the bolt and see if you can easily pull back the charging handle to extract the ammo?
If yes. Does the shell extract away from the rifle cleanly or does it just dribble out? If dribble out, check and see if there is good spring pressure on the plunger in the bolt face. Then again, you said the shells extract cleanly when manually extracted. Hummmm
Another possible reason could me misaligned gas port/gas block or fouling in the gas tube? Do you use WipeOut? If so, spray some down the gas tube and see if it foams out the other end by the gas block. Then again, you did say the bolt locks back on an empty mag.
How are the gas rings on the bolts? Have you checked to ensure they're not worn ie, if you extend them outwards from the BC and stand it on the bolt face, does it support the weight of the BC or does the bolt slip easily backwards into the BC?
The other problem could be that the timing is off ie the bolt is cycling slower than it can extract the spent case while the fresh round is already on the way up from the mag, lifting the spent shell and preventing it from extracting? Did you change the buffer to a heavier one or changed out the buffer spring prior to having these problems? Is the buffer tube loose?
I'm just grasping at straws. You might need to have a smith or a buddy who knows his AR platform to have a look at it.