The module supports 3 tags that all generate a Table of Contents.
The most popular is now [toc] since it is easy to type and works in WYSIWYG editors.
Various known issues with the Table of Contents module.
Teaser appear, FCKeditor accentuated letters, Back to top arrow, Filters interaction (JavaScript removal,) headers numbering, double numbering...
If you are using a WYSIWYG editor, it is not unlikely to add a <p> tag at the bottom with a character to make sure that you can place your cursor on that last line. The problem with that is it also adds a lot of space at the bottom of your header and footer in the CuteMenu.
The best is to turn off your WYSIWYG editor whenever you edit these nodes. Since only the administrator is likely to change the header and footer of the menus, it should be just fine.
CuteMenu has no global settings under the Administer » Site configuration. Instead, the settings are localized in the block and the menu items.