Brad,
Not sure why the SSL is showing as not valid. It could be an issue with our tool as well not properly detecting the certificate on your site. If it continues to be a problem in a few days, let us know. It may just be a propagation issue where we're not fetching a new certificate yet.
As for the logging in popup, try re-enabling that and the "Include jQuery" setting within the JFBConnect -> Configuration area and test again. That may include all the proper Javascript that you need to have enabled to get the popup to work.
I hope that helps, but if not, let us know.
Thanks,
Alex