There are several possibilities why your website has not recovered after an algorithmic penalty. Here are some of them:
Types of sites that don’t recover from a penalty
Sites with very little chance of recovery
– Those that used to rank by spam links.
– There is a possibility that actual ranking (which is normally low) is given to the site after the penalty is lifted.
Sites that need more work or have to wait longer to recover
– Those that have been dealt with a manual unnatural links penalty can also be dealing with Penguin.
– Google will have to crawl every link in the disavow file and this process could take several months.
– Google will have to rerun Penguin to determine if the disavow is effective.
– Backlink audits should be done each month whenever your site is hit with the Penguin filter.
– There is a possibility that Penguin will ignore low quality directory links, and there is also a chance that these links can affect the site negatively.
– You might also need to cleanup on-site quality issues as there is also a chance that they are affected by the Panda algorithm.
– Aggressive links disavowing, in some cases, can cause site rankings to fall because the good links were also included in the disavow.
Sites that have fallen victim to a flawed algorithm
– Good quality sites but are still outranked by low-quality scraper sites.
– Even if the unnatural links were cleaned up, the Penguin algorithm can cause Google to distrust a site.