Not that I'd know, but I've never heard of such a thing. I don't see the benefit of such a penalty anyway. I doubt it's an issue with the SE's.
To put it another way, being able to discern a nofollow penalty would be bad for the nofollow tag anyway - such blatant manipulation by the SE's of the use of the tag (in direct contravention for what they've stated is the intent) would lead to all sorts of mistrust.
Remember, google doesn't hire search people, it hires statisticians.
They'd be looking at nofollows to see if there's any signs of spam...or something. Then applying that....somehow, I don't know.
But just because they drop the nofollow links out of the current link graph doesn't mean they don't use that data for other uses. In fact, I'd be surprised if they didn't analyze nofollow links for some sort of data or indirect assistance with the serps. Or some other nefarious purpose.