This is driving me crazy as well. I have found (for the most part) that things are working OK as long as I do my showing and hiding on ANYTHING OTHER than my lowest subdivision level.
I will get some random quads that go to another polygroup and no matter what I do I can not get them to stick. The really bad part is this is also messing up the UV’s on my model for the quads. I had to take my lowest sub D level into Maya and fix everything back up. Now I have a base level model with SubD levels and correct UV’s saved out as an OBJ. If things mess up I just reimport this model back in to fix things. Not a cool work around but it is doing the trick.
Peace-NickZ. 