Although I'm a KDE user, I would think that you're right in saying that your menu configuration problem has to do with files in your home directory.
I suggest you create a new user and log into gnome using the new username. If the menus are OK, you could simply delete any .gnome or similar directories in your own home directory. Do this by logging out, then hitting alt-ctrl-F1 to switch to a terminal. Log in using your username and password and then do:
$ rm -rf .DIRECTORY-NAME
where you'd replace .DIRECTORY-NAME with the name of wherever gnome keeps its configuration files (something like .gnome?). The dollar sign just represents the prompt, it's not something you have to type. Only do this if you've first checked that the menus of a new user are OK.
Sorry I can't be more helpful about the name of which directory(ies) to delete, but the ones you mentioned sound like likely candidates. If you're feeling adventurous you could log in as the user you created to check the menus and see what directories have been created by gnome by typing
in the new user's home directory.
Once you're done at the terminal, hit ctrl-D to log out, then alt-ctrl-F7 to switch back to the graphical log in. Hopefully your menus will be back when you log in again, and then you're just left with deleting that user.
Careful! Doing this would also mean that you loose all other custom settings you've made to your desktop!