Jwvr,
We just released JFBConnect v5.1.2 today which has multiple Javascript conflict fixes, as well as a lot of other minor changes to improve some features. I'd recommend upgrading to that release and testing again. Specifically, in the Configuration -> Misc area, try testing with the "Include JQuery" setting enabled as that will setup a jQuery compatibilty layer that should fix conflicts with other extensions (and ensure the "Show 'logging in' popup" setting works.
I also downgraded Social Profiles
The v5.0.x social profiles will not work properly with JFBConnect v5.1. You should upgrade back to the v5.1 version of that plugin.
Thanks,
Alex