I notice a lot of themes passing the ‘edit_themes’ capability when registering their options pages with add_theme_page(). On multisite installs edit_themes is reserved for super admins (and if a site defines DISALLOW_FILE_MODS then not even super admins will have it). If you want regular admins to be able to see the options page, which you probably do, you need to use ‘switch_themes’ instead of ‘edit_themes’. Perhaps we need an ‘edit_theme_options’ type cap if we want to be discreet from switch_themes.