Nothing serious, but I have seen that most of the Cobra Commander's from the comic 3-pack (even the 'Con exclusive packaging) are missing the stripe on the right leg. I did pick up one (of 3) a few days ago that has evidently been corrected. Just a minor thing, but it's out there.
I When I got my comic #3, all of the Cobra Commanders from the case were still missing the stripe. I don't think this variation occured quite that quickly.
I don't know about nationally (though I would guess it to be the same), but around here the painted stripe Cobra Commanders appear to be the much later version and while less common, not hard at all to find.