Well, *if* Google is doing what it says and 'removing nofollowed links from the link graph' then thats what should happen.
I suppose it doesn't mean its true.
I don't have any cases of nofollowed links providing a ranking advantage; YMMV.
But - have you tracked links to see if you aren't getting reprinting or somesuch happening thats causing the rank bounce?
Or could it be straight user tracking, such that Google can see you are getting traffic so gives you more? That would lead to very short lived rank improvements :(