Clipping figured out

I have a Wildcat 22. First of all let me say that it's the most accurate, consistent reliable airgun I own and I couldn't be happier with it. It's my go to gun. The gun now has about 15K rounds through it. After I had it awhile I bought 4 of the stackable FX cups to quiet it down. That did a good job, but noticed with all 4 installed there was a slight clipping and my POI changed. Changed them all around, tightened, opened them up a few thousands, everything I could think of and same thing. So just used two of them and problem was solved. Then Neil offered his unit and I thought what the heck. Got his unit installed and it clipped BAD. Neil's unit is twice as long as the FX so now it's become obvious there is an alignment problem. Today pulled the barrel and chucked it up in the lathe. Put the micro dial indicator on the mating shoulder and spun it by hand. Sure enough. There is a .003 difference from one side to the other. So now I know the problem. Just not sure what to do about it. Guess I could just fire up the lathe for real and true it up. Maybe Ernest will chime in. 
 
Is the end of the barrel threaded, or just a sleeve which the moderator slides over? If it is threaded, pay close attention to the 90 degree face where the threads stop (closest to the trigger). As another test, get a very long 1/4-20 bolt, and turn it down to .217. Slide it through the moderator and into the bore until you have at least 2 inches in the bore. You will then be able to see how well the bore aligns with the hole in the moderator. 
 
I've done the same thing with my .25 Wildcat. I had an adaptor made (double male) so that I could screw it directly onto the stock shroud. Actually, I had 3 adaptors made so I could use the stacked shroud system on my 400, Wildcat, and 500 (when I get one). 
Here's a thought, just get a .25 end cup or open yours up to .25. I originally had a clipping issue when I used the adaptor so, I just used the next size up end cap and it solved the problem. Eventually, I ended up getting the other adaptors and switched them around until I found the one where everything lined up. Now, I'm using .25 end cap on .25 Wildcat and .22 end cap on 400. 
And, yes it did quiet it down quite a bit! I don't recall right now whether I'm using 4 or 5 sections. 
Tom
 
addwetooth. I believe the end of the barrel is threaded. As of now have not been able to unscrew the shroud.
Tom, that's a good idea and basically what I'm doing now. I've got two cups and the end cap all for the 25. If I continue to add cups making the moderator longer then the clipping returns. And Neil's moderator being longer still is completely unusable. As I see it the piece that screws onto the end of the barrel and has the shroud on one side and the moderator on the other has a shoulder that is not square. Only way I see to fix the problem is to true it in the lathe. Just don't know if its worth the trouble. 
 
"hsnmz"I think adding an additional moderator adds weight to the end of the shroud. Which pulls the shroud downwards causing the misalignment issue and clipping.
I had never experienced clipping problems first hand until I got the Ataman. There was a couple of things I noticed that were different to my other air guns that I believe to contribute to the issue:

First is that it has short barrel threads. It has less than half the number of threads of my other air rifles. That gives it more room to move. 

Second and and perhaps more important is that there was visible alignment issues on the first two I received. I could see where the shroud tube did not run parallel to the barrel. I am guessing this is your issue as problems like that become more apparent as the shroud gets longer.

As you have the issue with the NC LDC too, I think your alignment issues will be on the end cap threads you are attaching it too. The are probably not aligned properly with the barrel.

The easiest way to prevent the pellet from hitting the baffles or end cap is to make the hole slightly larger. If you have a drill press then this is a fairly easy job. If it is new then just ask the store you bought it from to help you get it fixed as it is a factory fault. 

If it was me, I would send it to a pro to fix if it was out of warranty.