Yup, it's been discussed before

The 3.2 release has the ability to fix this, but we haven't really documented it much because we threw it in the last minute. It will take a minor amount of code to add the button, and hopefully, you're up to the challenge. The problem has to do with using Javascript inside of a Javascript pop-up window.
I'm assuming you're simply using the JFBCLogin module and placing it in the pop-up that RocketTheme uses. If that's not the case, just let us know.. if you're adding the {JFBCLogin} tag to another Login module, it's basically the same steps. Anyways, edit the /modules/mod_jfbclogin/tmpl/default.php file. At line 42, you'll see:
echo $fbClient->getLoginButton($buttonSize); ?>
You'll want to replace that with the following:
<a onclick="jfbc.login.login_custom()">Login With Facebook</a>
This will be a simple text link, but you can add any image in place of the Login With Facebook text and that will be the login button. If you need more help with that, let us know. In the next release, we'll be adding an option to use this login ability instead of the standard Facebook one. We'd love to hear your feedback, but so far, reports have been good with this method.
Thanks!