JFBConnect and the SCLogin module do use jQuery and Bootstrap. Please set the "Enable JQuery / Bootstrap" setting in JFBConnect and the SCLogin module to 'yes'. When our extensions add those libraries explicitly, we do it in a specially namespaced way so that other extensions shouldn't be able to break our compatibility.
When that setting is 'no', we rely on the defaults included in Joomla, which can be overridden by other extensions as you've seen.
Hopefully, flicking that switch should fix your issues with JFBConnect. Please let us know how it goes.