POI change when changing magazine

Possibly damaged pellets while cycling through theagazine. Single shot tray recommended in this case or try new magazines that hasn't been alteted or modified. When they're modified good chance the pellet doesn't go into the barrel perfectly straight smashing the skirts as you close that bolt feeding canted pellet into the barrel due to oversizing leavening the index separating "gears" in the magazines especially when shooting short pellets. Thats why I don't recommend modding magazines.
 
I will try to switch out 4 magazines with the same pellet in each of magazines next and report back. Here's what I did the last time that I had the chance. 

50 yard target, Magazine A held pellets, Magazine B held Hybrid slugs. I had previously shot each on different power levels with very good groups. 

So I started off with Mag-A on power level 1 with very good groups of 8 shots on a fresh fill to 250 bar. I switched to power level "max" and then replaced with Mag-B. Took 8 shots. first shot was way off target (not super surprised) and the rest grouped nicely albeit at a different POI (as expected). I then filled to 250 Bar, switched to Power-1, and then switched back to Mag-A that was reloaded to capacity with pellets as before. POI should be back to original POI, right? Not even close. Off by more than 1 MOA of elevation and windage. Pellets and slugs were unsorted. Next time, I plan to sort the ammo to rule out weight/diameter differences.

Any thoughts?

Thanks
 
If I understand, you are getting getting good groups, but a changing POI. With no other variable changed, it does suggest a magazine related issue. But, there might not be anything wrong with the mags, because in some rifles (don't know what rifle this is) the insertion of the magazine can slightly alter the barrel alignment it everything is not properly secured. One MOA, or a half-inch at 50 yards can be the result of a shift of only .001". Usually, if a magazine alignment problem is causing significantly damaged pellets, the accuracy will be poor, with wide flyers, at least that has been my experience. If the magazine alignment is not off much, but yet not perfect (very common), then accuracy will not be as good as when loaded single shot, but not terrible either. 
 
I am referring to FX Impact MK2 with STX pellet liner, .22 cal. And yes, I am getting good groups but with changes in POI. sometimes within same magazine being used.

Well, with an FX Impact, good luck. FX has had some very innovative designs, and they work kind of okay. If you want an FX rifle that holds its POI, get a Royale or Boss. Sorry, but that is my experience with the brand. Had a Crown, shot great at a given moment, but relying on it to shoot the same the next day was an exercise in futility. I have had a Royale 400 a couple of years, and it has been rock solid. In fact, I dug it out of the cabinet just this afternoon when a squirrel attacked our bird feeder. Rifle had not been shot in several days. Squirrel gave me a shot at 30 yards, and it was right through the brain. I would have had no confidence in the Crown in the same circumstance. Good luck.