For the SCLogin module, we have a whole theming system you can use to make sure you're CSS or PHP/HTML changes aren't overridden when you upgrade. For more information, see:
www.sourcecoast.com/sclogin/documentation/themes
We always recommend upgrading the SCLogin module when you upgrade JFBConnect. Actually, it's part of the upgrade process, so I'm not sure how you are installing JFBConnect *without* upgrading. If you're not using the JFBConnect installer, that itself could be part of the problem.
As to your other notes.. the URL and the 'flooding' message in general point to the fact that you're using another SEF extension, likely sh404SEF. You'll need to configure your SEF extension to 'skip' JFBConnect URLs. If that doesn't help, disable it altogether to test if that at least fixes the problem.
Beyond that, please let me know if this is happening on other sites and what site you're having issues with so we can test.
Thanks,
Alex