In the Google Hangout this past Friday on Google+ with John Mueller, John discussed how manual actions and algorithmic penalties are different. In short, if your site was hit by a manual action, it may also be hit by an algorithmic penalty and being released from a manual action might help but if your site is also hit by an algorthmic penalty, then you will have to wait for the algorithm to update.
At the 10:55 mark into the video, John answered:
Are we correct to assume that if we have recovered from a manual penalty then we need to build Googles trust again even though you say you hold no grudges in the algorithm? If so what metrics should we be looking at to help us?
It's hard to say there. It kind of depends on what specifically what’s happening there.
But in general, if a manual action is resolved, then that manual action has no effect anymore.
And all that's left is really that the rest of our algorithms how they interact with your website. And some of those algorithms might be looking at similar things that the manual action was looking at.
So if you've cleaned things up significantly, then sometimes that just takes a while for all of these algorithms take that new state into account. And of course, like I mentioned before, it's not the case that you're locked in any position. You can really work on your website across the board with pretty much everything to really show that your website is essentially the one that we should be showing for these types of queries.
But, obviously, that's kind of broad and really hard to turn into something more specific to work on. So one thing I do in a case like this is really get a lot of feedback from your peers. So go post in the webmaster help forum on our side-- maybe in other webmaster forums-- and really get feedback maybe really the hard kind of feedback that you don't want to hear from your peers so that you kind of have something that you can work on that you can focus on moving forward. There's no one answer that fits all websites for that.
Here is the key point that many SEOs don't get: "And all that's left is really that the rest of our algorithms how they interact with your website. And some of those algorithms might be looking at similar things that the manual action was looking at."
Here is the video embed:
Forum discussion at Google+.