First thing I would do is to set up the center station of the loader. Check and be certain all is correct.
Very hard to determine exactly what you mean. Is the punch simply NOT reaching the bottom to press the wad against the powder ? Or is the wad being pulled back out from bottom by the seating punch ? Or is the wad being " squashed " and expanding back, while never having been pressed to the bottom ?
I believe these issues can be fixed by getting you allen wrench, wrench and screw driver and resetting the center station. While you at it check your wad guide fingers. It is not very dificult to change for STS or AA hauls. Really very simple.
I also load the Double A wads, OR windjammer wads, and have ALWAYS used AA hulls. Saving the STS for when my AAs are used up.
Added : You got me ? I have 3 MEC 600 JRs setting here I use daily, and I do load AA hauls mainly. I load 12 ga - 20 - and 28. No problems whatsoever. Just loaded 500 12 ga. AAs for this weekend.
Added 2 : Two of them are MK.5s. I am wondering if you may be compressing the air below the wad, and it is NOT venting it past the wad, so pops back up when the punch pressure is released. If you look at most plastic shotshell wads they have three grooves in the base wad portion. Hence are normally meant to allow blow by. I honestly have never had this problem. I load both the Red AAs, and the " Silver Bullets " as we call them. And I do use both Clay buster windjammers, and the true windjammers wads.
What happens if you just shove the wad down with your little finger ? Does it pop back up then ? That should eliminate anything to do with the press and may point to compressing the air. Now for years I have watched the inside of AA hulls. Unlike some others once fired they get a roughness inside the case walls. This was a big difference from the old AAs and the more modern ones. Also leads to a short hulls life. Compare this to your STS and you will see what I mean. You are using the RED AAs right ? I have 55 gallon barrels of RED and Silver hull I have been working through.
* A cool side note, I have shot with the man who patented the Plastic shotshell wad for many years, back in the early 60s I believe is when he sold the patent to Remington.
If needed you can hit my email here. I have tried to duplicate this and can not so far. I can compact the wad column by pressing it too deep, and if allowed to set a moment it expands back. But, the base does NOT raise off the powder charge. Must be compressing air under the wad if it is popping back up after the punch is lifted. OR the wad is getting enough friction on the punch to pull the wad. If this could be the case try polishing the punch. Maybe even some auto wax polish to slicken it up.
While I enjoy figuring out things, I know this is aggravating for you. Sorry.