I was at the range shooting last night zeroing a couple ARs.  The first was an 11.5" BCM SBR that ran perfect.  

The second is a newer build and it was having problems feeding using the same 20 round magazines.

I would insert a mag all the way, tug it, release the bolt and it would ride over the top round and not load.  

I was having the exact same issue on both 20 round magazines, a Colt one and a Magpul.  

I tapped on the mag and messed with the rounds and eventually it would work but then I did get some jams and it would fail to lock the bolt back on the last round.

I was shooting Tula and PMC X-TAC 5.56mm NATO 55gr FMJ-BT M193.

I took it home, tried dummy rounds and live rounds and had the same issue.

I tried a 30 round mag and it worked just fine.

Why would two magazines work fine for one AR but not the other?

I recently swapped the BCG on this and before that the only issue I had was failure to lock the bolt back so I reduced the buffer weight from an H to a CAR.

Any ideas?

This is the current build:
Ballistic Advantage AR-15 Enhanced Lower Receiver
Ballistic Advantage AR-15 ENHANCED UPPER RECEIVER
Radian Raptor Ambidextrous AR-15 Charging Handle - FDE
VG6 Precision Epsilon Compensator - 1/2x28
Ballistic Advantage Performance Series 5.56 Hanson Mid-Length Barrel with Pinned Gas Block - 16"
Aero Precision AR15 15" ATLAS R-ONE M-LOK Handguard - Anodized Black
Geissele Super Dynamic Enhanced (SD-E) Trigger
Aero Precision Lower Parts Kit for AR-15 (Excludes FCG, Trigger Guard, Pistol Grip)
Magpul MOE Slim Line Carbine Stock - MIL-SPEC - Flat Dark Earth
Magpul MOE Polymer Trigger Guard - Flat Dark Earth
Magpul MOE-K2+ Pistol Grip - Flat Dark Earth
Magpul Picatinny Ladder Rail Panel - Flat Dark Earth
Aero Precision Enhanced AR15 Carbine Buffer Tube Kit
Radian Talon Ambi Safety 2-Lever Kit - FDE
Ballistic Advantage 5.56 COMPLETE BOLT CARRIER GROUP, NICKEL BORON

It could just be me, but I didn't see which lower receiver you're having issues with being listed. Here's one thread: FTF. Another, although a Grendel: FTF Grendel.

Oh, left that off, it's an Ballistic Advantage AR-15 Enhanced Lower Receiver, same as an Aero M4E1

Can you visually check to see if it looks like the magazine is presenting the round too low for the bolt face to catch it?  Are you able to try a different lower and see if that works better?

Did you try switching  the complete uppers uppers out with one another and then running the mags to see if the issue followed the upper? If the issue does follow the upper then look at  the bcg, If the issue doesnt follow the upper then look at the Buffer and spring of the lower. Just my first thought.