Unfortunately Steam sometimes returns more (sometimes less) games than you own. I have yet to discover why this is, but if you connect to the steam community site you will see the same problem. My experience is that eventually they spot the mistake and your games will be correctly returned.
There are two reasons for this; 1. The game does not have (or does not publish) its achievements 2. Steam sometimes fails to return the correct list, eventually they spot the mistake and your games will be correctly returned.
Visit https://steamcommunity.com/ and login with your Steam user name and password. After logging in, examine the URL address, it will either look like:
a) http://steamcommunity.com/id/xxxxxxx/home
or
b) http://steamcommunity.com/profiles/11111111111/home
(a) The Custom URL is located where the xxxxxx’s are, and (b) the Steam Id is located where the 111111’s are.
To save those settings with STeamAchievements then just enter one (or both) of those values into the Settings and press Save. If you've entered the details incorrectly then you'll be notified.
Form more information, visit the Steam names & user IDs page.