A Google Webmaster Help thread has a story of a site that is trying to disavow and remove all the bad links pointing to his site.
The interesting part is that even when he does, will it help with his site's rankings?
The goal of this webmaster is simply to remove the manual action, but Google's John Mueller tells him he also has algorithmic trust issues.
looking at your site's history, it looks like you've done quite a bit for quite some time, and it looks like our algorithms have picked up on that too. So while resolving the manual action is a good way to start, you need to keep in mind that it can possibly take quite some time for our algorithms to regain trust in your site even after that.
I see this happening a lot, webmasters aim to remove the manual action and do but then the rankings don't improve. The reason is likely do to algorithmic actions taken on the site.
That being said, it is interesting to see how Google words it.
The algorithms seem to have lost trust over time. The manual action is a "good way to start" but the algorithms need to "regain trust" in the site for there to be an improvement - which may take some time.
Forum discussion at Google Webmaster Help.