Dave,
Help is no problem. Unfortunately, you've got us a little stumped there. First off, though the login box is being loaded in a pop-up, it's not being done through an iFrame, so don't follow any of the instructions in the post you linked. I can see where the similarities lie though.
With that said though, I don't know what's 'wrong'. I see the button, but when I click it, nothing happens (assuming that's what happens to you). There are no Javascript errors, everything seems to be loading correct, and everything 'looks' good.. just nothing. Can you try putting the JFBCLogin into a module that isn't in the pop-up and see if it works there? That may help us narrow down the problem.
Finally, and unrelated, but you'll want to disable JomSocial's Facebook integration. There shouldn't be 2 things trying to manage FB Connect, or you'll run into issues. To disabled, just remove the API/Secret keys from the JS configuration area.
Please let us know if the above test with a standalone module works, as we're curious as to what's going wrong. Sorry for the troubles, but we'll get you fixed up!