Hi, I don't have an easy answer for this. Gantry and our Gantry based themes do not use the wp_footer() function at all, we have a completely different theme structure than most WP themes.
You can add scripts into the Gantry head by placing them in the Gantry theme js folder, then adding:$gantry->addScript('name-of-file.js');
Into the <head> section of the theme index.php file.
I have no idea if this will solve your issue or not. Some plugins just are not compatible with Gantry unfortunately.