When you uninstall JFBConnect, the database tables are not removed. Because we store information about how a Facebook account is 'mapped' to a Joomla account, as well as all the settings, we don't want to destroy that information when user's uninstall. Most users who uninstall are simply going to be installing an upgraded version of JFBConnect shortly after and loosing that data or having to reconfigure would be painful. If you really need to remove the tables, you can go into your database and remove any xyz_jfbconnect tables (there are 4 of them).
However, that really shouldn't be necessary. Can you give any more information about what is happening? We've never heard of settings reverting before. Is this after some time after saving, or do the values you want never save? Are you using some custom admin template other than the default Joomla one? If so, please try going back to the original and try again.
Other than that, any information you can provide would be very helpful for us to get you the best solution.
Thanks!
Alex