You won't loose your settings if you uninstall JFBConnect. We leave everything intact, or that'd be a nightmare. Our installer does update the database. However, if you're using the Joomla Update Manager and checking there, you'll need to use the "Purge Cache" button and then "Find Updates". That should properly work. Joomla only looks for updates periodically and installing a new one outside of the Update Manager doesn't cause it to clear itself. That's a Joomla bug, not JFBConnect, but completely understand how it's confusing.
Hope that helps!
Alex