Did you make changes to the index.php file? The main top menu should pull the items and display from your main menu items unless you remove them from the index file (at least that is the way I understand it).
Can you enable the main menu module and put it somewhere else, like in the left position or something, just to see if t works there?
If you made changes to the index file, you can copy that back from the original template files to get it back.
If you still need help I can take a look if you PM me with your login. Or just show a url so we can try to help figure it out.
Cheryl
