We don't load any bootstrap.min.js file on your site. We do use a file called jq-bootstrap-1.8.3.js, which has a specialized version of jQuery and Bootstrap that's specific to JFBConnect. You can disable the loading of that file with the "Include jQuery / Bootstrap" setting in our Configuration area. However, only do that if you are already loading jQuery and Bootstrap into the page on your own.
Our specialized versions of those files are setup in a way that is invisible to other extensions, so that it can run alongside them without causing conflicts. I'd be surprised if that file is what's causing your issues, but let us know if so.
Thanks,
Alex