I've found that even when logged in as root, only certain things will start when clicked from the menu.
First: I hope that you log in as root only when you really need to. Using root account to do normal tasks can easily lead to unexpected problems when you try to run programs as normal user.
Second: Check that you have the menu package installed. If you don't know how to check this, try "dpkg -l menu". If the output starts with "ii" (two i's), then the package is installed.
If the menu package is installed, you can try to update the menu by using "su" to become root (note: you don't have to log in as root to do administrative tasks) and typing "update-menus". Then leave the root account by hitting Ctrl-d.