So in essence, you are saying that the bolt will not retract back far enough into the receiver for the bolt lugs to get behind the bolt catch, when pulling back all the way on the charging handle, right? If this is the case, there is something in your buffer tube that is keeping the buffer from moving all the way to the rear. If this is a A1 buttstock, the problem could be you have an A2 buttstock screw installed. If it is an A2 buttstock, then I would be surprised to find out the screw it too long, but I guess it could be a possibility.
Do this, break apart the upper and lower, remove the buffer and buffer spring and see if you can find anything wrong with the inside of the buffer tube that would keep the buffer from moving all the way back. Compare the lower, carrier, and bolt to your other AR and see if you can find anything that is different, that could obstruct full movement of the carrier.
As far as short stroking goes, refer to it as short recoil, or Chuck will get on your ass and make you feel like an idiot. Short recoil/stroking can be caused by all sorts of things and can be very hard to diagnose and cure. Basically, it is caused by either the gas system not getting enough gas to the carrier to push the carrier/bolt all the way back, or from something rubbing against or obstructing the full movement of the carrier. Would need a lot more info to diagnose what is causing the short recoil issues, like ammo used, brand and model of rifle, etc. That said, if I am correct in my initial assesment at the top of my post, then I doubt it is a short recoil issue.