I think the answer here depends on whether or not you have actually been penalized and why the site is dropping out of the SERPS. Do you have a warning in WMT? If not, then you're probably not penalized.
It's unlikely to be Penguin because Penguin did not refresh lately. Similarly, Panda did not refresh on the days you mentioned. So, it's not likely a penalty but rather some type of site structure issue.
Is there duplicate content between the subdomain and the root? If so, then Google will choose one as the owner and not show the other prominently. Any issues with robots.txt? Are the canonicals set correctly? Any chance of accidental noindexing?