The SCLogin module uses the core Joomla user component to actually authenticate users. The SCLogin simply has additional features as a front-end to the user functionality, as well as support for our JFBConnect social network authentication features.
Since the standard Joomla mod_login module isn't working as well, it sounds like there's some other underlying issues with your site. I hope you're able to determine and solve that, but I don't think it's related to the SCLogin module. If you get the Joomla login module working but SCLogin still doesn't, just let us know and we'll gladly help investigate further.
Thanks,
Alex