Jeroen,
First off, in JomSocial, you have their Facebook Connect functionality enabled. That should be disabled. For more information on how to best integration JFBConnect with JomSocial, please see:
www.sourcecoast.com/jfbconnect/docs/thir...ration-for-jomsocial
As for the popup in the top right, I'm brought to the JomSocial home page. I don't see a popup at all. However, if it's just disabled for now (since it wasn't working), I'd recommend trying the new "Login Button Type" setting in the SCLogin module with version 4.2.3. Change that from "Javascript Link" to "Text Link" and change the Text Link box to "Login with Facebook". Then, you'll get a bare link in the SCLogin module with that text.
The Javascript button can have issues when called through other Javascript functions (like AJAX), and the text or image link method is how you get around that. If the text link works, then you can use an image that looks identical to the Javascript method and it will act properly.
Hopefully that helps, but if not, just let us know!
Alex