hmmm.
normally they do protrude a little, like ~0.5mm ish but you're saying it sounds like much more than that.
can't recall if i've mentioned it before but if not it's worth checking the mag/ammo, a weak mag or some ammo brands can cause the stack to bind up causing jams that a better brand of ammo/mag would solve.
that's mainly if you're using mid caps, hicaps tend to not be quite so susceptable as they're single stack and much shorter column.