Good morning Nitrah.
I have the same problem on an early 12 gauge Tournament Skeet.
I load a pillow soft 7/8 oz load using Federal papers with a Win 209 primer on a Mec 8567 Grabber.

I adjusted the powder tube height so as to set the primer at its absolute highest point (least amount of depth).
I scored the tube each try and backed off after finding which height setting was not quite flush.

Did it work? While I believe it will take the issue of primer depth out of the equation,
I don’t know for sure because at the same time I sent my gun off to the stockman for a new stick of wood.
Time will tell.

[Linked Image from i.imgur.com]


[Linked Image from i.imgur.com]