Don, is the first one in your post the same one that drops free when empty?
Is there any sort of outward "flex" to the body of your mags? Perhaps it's mis-shaped (as you said, "sticks halfway out" when empty) causing it to hang up in the well.
I suggest using a straightedge and make sure it's not bulging even slightly, with and without ammo. Also check for any protruding surfaces on the mags and in the well.
Something is dragging in there...