fathom - 6:42 pm on May 6, 2013 (gmt 0)
Therefore, I've put nofollow on those links and am now waiting to see if it has a positive effect when Google reruns Penguin.
Purplekitty, PENGUINized links are links dropped from the link graph... that's why you lose ranks... adding rel="nofollow" prior to losing any ranks will have the precise same loss impact (assuming those links generated the ranks)... thus adding rel="nofollow" after PENGUIN has already dropped them from the link graph will only maintain your current status quo "as is".
Additionally, Google re-RUN of PENGUIN only allows Google to add more violations to the mix e.g. adding different ways to detect such violations... I'm sure if they have lots of false positive they could tweak PENGUIN and prevent those false positives but that is usually preceded by a Google statement about the false positives.
Don't take my word for it... go to the video meetups and ask Googlers.