Lemme say I'm not an AR wizard, I have a working knowledge of these guys, but I'm not expert.  I have a Colt SP1 and a range of upper.  7", 11", 16", and the original 16" A2 upper, as well as a Colt 6920 A4 upper.  

So I went and shot it today, and it had a lots of issues with the 16" A2 upper and the 6920 upper (M16 bolt), It seemed like there were two issues, it would load the first round that I manually loaded, and the second round it appears the bolt wouldn't go back far enough and it would just close empty (without loading a round), or it would also not load the next round completely, ie it would start to load the next round but would stop short of going into full battery..  This happened on both 16" uppers.  

Now swapping to the 14" colt A2, or the 11 CMMG A4 with an M42000, or the 7" CMMG A4, all functioned just fine..

I'm not particularly fond of the 16" uppers compared to the short ones, but I would like to know what the issues is.  From what I can tell the lower, it has a Standard H buffer in it (it's not marked so I could be wrong).  I prefer the short uppers so I don't want to modify the gun where as it would shoot the long uppers and not the shorts, or put any stress on the lower.   I tried an H2 buffer and the same problem existed.

I suspect the buffer or the  gas systems configuration in the two 16" uppers.  Does anyone have any advice they can give me here.  

Here is a video of the 11" with m42000 and the 7" upper.. I didn't take one of the 16" but they functioned badly..

https://youtu.be/u4MJvUk5MU8

https://youtu.be/vU1x5ngUXNg

Check the gas key on the bolts for both uppers.

Sounds like a buffer/spring issue.  Are you using the same bcg on all the uppers?

More than likely. I've been very lucky, I run the same buffer/spring combo on all my uppers from 10-1/2 to 18". No problems.

 

Going back and forth from a standard to a H buffer should not be an issue for any of those setups.

I would check the gas systems.

I agree. Sounds like its short stroking. Could be a combination of things here.

Yes the same buffer and spring on all.  The thing that bothers me is that my 6920 upper functions perfectly on my 6920 lower... There really shouldn't be much difference other than the bolt..

What exactly should I be looking for here?

Out of curiosity, what ammo were you using?

I had two different BCG's where one bolt on the gas key broke. Check that they are tight.


 

WPA...

Is it the Zinc coated Steel, Poly Coated Steel, or their WPA Gold real brass ammo?

Are all the chambers the same? IE 556 or Wylde? If you have any truly chambered in 223, the steel can be unhappy with that sometimes.

It does sound like a gas issue (having not actually seen it for a better determination). Since you are changing Uppers, what is different in everyone of them that could have a huge impact on how the gas operating system might be preforming? Yes that is right, the BCG Key has to deal with a different Gas Tube on each and every Upper as the gas tube stays with the Upper whether you run the same BCG or different ones. Check each gas tube for proper alignment and fit. Make sure they are not bent, misaligned, or damaged on the end where it is flared slightly to create a momentary seal in the BCG gas key.

Lastly, I would pull the bolt and check my gas rings to make sure they are not all lined up making a big slot or worn while I am checking the operating system.

Zinc coated stuff.. I'll check out the gas system and the bcg fit on the two uppers that aren't working.   I'll everyone know if I can figure it out.

If your near the west side of town I'd be glad to help. Not that I'm an ar god or anything, but I have several lowers we could try your uppers on and some land at the house we could test them out.