It happens with both the cheapo new Sig mags and the brand new Mec Gars I got after buying the gun. It is actually worse with the mec gar mags than the Sig ones. Unfortunately one of the Sig mags doesn't drop free well, while the mec gars do. I'm wondering if I'm just seating the mag with too much force. I'm used to shooting 1911s with magwells , so my regular reload involves seating the mag pretty forcefully. Still I wouldn't think I would be able to hit it hard enough to jumble the rounds around in the mag.
I run the MecGar mags in production loaded with 10 rounds and I seat the mags hard enough that on slide lock reloads it releases the slide. And I have never had the problem you describe. I have two of the current production checkmate mags and they have jammed pretty much every time I have tried to use them.
What also confuses me is that you appear to be saying your MecGar mags have weaker springs than the checkmate mags. That is exactly opposite of what I have observed. The two checkmate mags I have when fully loaded exhibit much less pressure against the feed lips than my MecGars. So in short I am baffled.