How are you adding the custom Like code? Are you using the iFrame version or the Javascript version? We use the Javascript version, which could explain the difference.
Also, I do only see the Like button at the bottom of the page, with the Twitter, LinkedIn and G+ buttons. I didn't see you mentioned the Like Box (Fan box) as well. Looking at the code, you're correct, I don't see the tag for that module anywhere.
Can you let me know, just to clarify everything:
* Can you see the Like *button* at the bottom of the article?
* Where should the Fan Box be?
* How are you including the Fan Box, with the JFBCFan module or the {JFBCFan url=xyz} tag?
Thanks,
Alex