Any new info on this, or a temporary workaround? This just started happening to me, and its making it impossible to profile my game correctly, which is kind of a problem. Is the unity case number you mentioned for this specific issue, because if so, I can add my voice to the "please get this fixed" chorus to unity.
-Sean
Update:
and just like that, to spite me, it stopped again... so not urgent, but I'd still be happy to help bug unity to get it resolved if that helps at all (assuming mine wasn't just a freak occurance).