It will compare your profile with other trackers to try and find which games we are missing achievements from. Usually this is due to earning achievements in family shared games or demos/free-to-play games that you no longer have access to. They don't show up on your list of games so this is why the site misses them.
Once you know the specific games that are missing there's an option to force a scan on them by providing the App IDs under Tools on your account page. The above tool will provide a list of IDs that can you can use, if it is able to detect them.
I concur we x3sphere steamhunters is one of the best steam achievement tracking sites. ALso the reason it is different on your steam profile is that steam only tracks achievements for games that are not restricted.