Hi, the footer color changer in the template settings is linked to the footer, copyright and menu sections. To change that, what you'll need to do is go into the Gantry plugin folder - it's in the plugins folder in 1.5 and the libraries folder in 1.7. In that folder, open the features folder and find styledeclaration.php. Copy this file into the features folder of your template, this overrides the original file and you don't want to make changes to the core files.
Once it's there, open it up and find$css .= '#rt-footer .rt-container, #rt-copyright .rt-container, #rt-menu .rt-container {background:'.$gantry->get('footercolor').';}';
Remove #rt-menu .rt-container from the code and the comma that is right before it. That will disconnect it from the template color chooser and you can then apply styling via CSS. Hope that helps.