If you're using the RokBox plugin to show the SCLogin module, that's the issue. The Javascript with RokBox conflicts with Facebook's login button. However, if you edit the /modules/mod_sclogin/tmpl/login.php file, you can find a commented out section which explains how you can replace the normal Login With Facebook button with a custom link or image. Look in that file and make the changes noted there, and you should be good to go.
If you need more help or explanation, just let us know!
Thanks,
Alex