I'll need to do further testing to get back to you with a proper answer on that. it happens rarely (not to mention in the heat of battle), so I let it slide/forget about it, but a couple of days ago it happened.
The up side is that most of the time it does damage, but the down side is that it's rare so I'm not sure of the conditions for it actually happen. I have a video of it happening against Mewtwo (which I'll need to upload), but then when I do the super again after, it does damage!