In May 2013, Google rolled out the second iteration of its Penguin algorithm update, causing issues for a wide range of websites that were affected by 'algorithmic penalties' - that is, they saw immediate drops to traffic because their link profiles fell on the wrong side of what Google decided was now acceptable.
This update affected sites that had done anything from blatant link spamming, to what had been considered acceptable practices such as guest blogging with contextual anchor text links, online PR submission where the syndicated releases could get picked up by any site that wanted them and directory submissions using anchor text within the business name.
Sites affected by Penguin 2.0 will not have seen a recovery, even if they have taken all the necessary steps to clean up their link profiles. This may also be impacting their ability to 'recover' from the effects of other Google updates, including Panda, even if, again, they have fixed any outstanding issues.
Unlike the Panda algorithm which Google has regularly refreshed since it first rolled out, enabling sites to recover as quickly as they can fix issues, Penguin refreshes are rare as ostensibly Google has struggled to get Penguin 3.0 to work to its liking. However, in a recent video Google did say the next update would "likely be launched before the end of the year" and that webmasters will find it a "delight." (via Webpronews)
For our part, we're hoping the update comes soon as we expect to see sites impacted by both Panda and Penguin that have only made slight recoveries improve their traffic once Google acknowledges that their backlinks are now fine too.