Plugin conflicts are usually the first point of call when elements disappear from the admin area. So this would be my first suggestion to rule out completely. If you’re reluctant to do it on your main site maybe set up a local install with the theme on and test that to ensure its not a plugin conflict.
This is exactly how I see the theme settings options display within the restaurant theme – http://screencast.com/t/7SNWsFDGKrVm
If you’re able to please can you screenshot your admin area so we can see what options are available and if there are any other restrictions showing. You’re definitely an admin level user on the site?