Bryan,
The comment box at the bottom of the page you said is bugged actually worked for me. However, that comment box isn't even coming from JFBConnect. It looks to be coming from another plugin on your site altogether. Additionally, that other extension is re-including the Facebook Javascript library which *can* conflict with JFBConnect's login functionality or could (though unlikely) be causing the comment box not to display in some cases.
I'd recommend using the social configuration area of JFBConnect to add the comment box to your content and disable the extra comment box plugin you seem to have installed.
I hope that helps, but if not, let me know.
Thanks,
Alex