Anthony,
From a quick look at the code in that Javascript, it's re-loading the Facebook Javascript library and initializing it in a way that's conflicting with JFBConnect's more advanced features. You'll need to either disable it's inclusion of the Facebook Javascript library (the all.js file) or disable the Like button feature altogether. I'm not sure of any other easy way to make them compatible.
Hopefully, there's an easy setting to do that, but I didn't look deeply enough at their code to understand how it's configured.
I hope that helps explain, but if not, let us know.
Thanks,
Alex