Measure the feed lips across, I don't have a 96 mag handy but all the other .40 cal mags are wider in that area.
What that means is the narrower 9MM round will be setting higher in the magazine, so when the weapon cycles, the slide has to push all the rounds back down, then when feeding, back up again.
I've had good luck reforming the feed lips, but with the ban expiring, I find it nearly pointless except for experimental purposes.
I can't leave things alone either...