It usually goes away after 1 to 3 weeks. But once it does everything in your account should be normal if you’ve made the correct changes.
I have trouble seeing the logic in that statement. If Google is penalizing you it is because your site is receiving an "unnaturally" high number of clicks. If you then correct the penalty, as you have, then the number of clicks you receive should drop significantly, as there are no, or at least far fewer, "unnatural" clicks occurring. To claim that everything goes back to normal suggests to me that either your layout changes had no impact or the impact was insignificant in terms of the penalty.
AdSense is rumored to apply penalties quietly and progressively. If you have been penalized before with the "double click" penalty and things returned to "normal" and now you have been penalized again a second time and now after attempting to make more changes your penalty is getting more severe, this could suggest that all your changes have had no impact, or that finally your changes have made an impact and you are now experiencing the "natural" state. The later is the more desirable state as the former could signal far more drastic penalties to come. But all this is speculation, because without any formal notification you really have no way of knowing anything for sure.
The changes in RPM, CTR, CPC your are experiencing could simply be extreme market changes. So far today my RPM is running at 1/4 my average, I've had a few really bad days this month, followed by normal or good ones. So again, there is no way to Know for sure.
What are your stats saying, how is your coverage? Is your CTR similar and stable across all ad-units/pages? Are you seeing different areas of your website being impacted more or less?