Imagine you work incredibly hard after receiving one of those manual penalty notifications to lift that manual penalty. You finally hear back on your reconsideration requests after months of work and Google gives you the good news, you're manual penalty was lifted.
You sit back and say - I'm back in business. But then you watch the orders, phone calls, leads and traffic and none of it increases. It just stays the way it was prior to the penalty. What a let down.
Now you go to the Google Webmaster Help forums for clarification and a Googler tells you, you also have an algorithmic penalty that you need to work on. What a let down!
That is exactly what happened to one webmaster in this Google Webmaster Help thread.
Google's John Mueller, in the nicest way possible, breaks the news:
Congratulations on getting the manual action revoked - that's always a good step :). Looking at your site now, it seems that some of our algorithms still aren't as happy as they could be. To some extent, it can just take time for us to recrawl, reindex, and reprocess all of the URLs and signals that we have to look at, so I wouldn't assume that your changes aren't appreciated (by our algorithms & your users). That said, being complacent and just waiting probably isn't a good strategy either, so recommendation would be to continue looking at ways to make your website the absolute best of its kind. Other parts of our algorithms will definitely pick up those kinds of changes (and your recent changes) faster, and if users love your site, they'll come to you with or without search engines. Good luck in 2013!
Forum discussion at Google Webmaster Help.