Phil,
JFBConnect added server side authentication options for Facebook in the v5.2.2 release. In the Configuration -> Parameters area, disable the "Show 'Login Credentials' in popup" setting. Frankly, the setting names in there are a bit confusing for the popup options.. but disable that, and you'll be enabling server side auth for Facebook.
Both Twitter and Google+ already use server side auth. We're planning to add popup options for those networks at a later date.
I hope that helps, but if not, just let us know!
Thanks,
Alex