Menu Items from nodes showing twice

I am using this method to create menu items for nodes I am creating:

http://drupal.org/node/141845#comment-229387
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For menus based on taxonomy check out taxonomy_menu module: http://drupal.org/project/taxonomy_menu

About creating menus in general: create a new empty menu in /admin/build/menu and enable it in /admin/build/block.

Now, when creating or editing a node, there's a little link "menu settings" at the bottom part of the node-editing-form. This is where you can manually inject this node into the menu of choice, give it a name and title and order (by weight).
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Everytime I add a new node using this method, the link in the menu shows up twice. I am suing taxonomy and need to continue using it for the access control and themes. I think the Categories module worked better for navigation, but doesnt have the same features as the tax_menu, TAC, themes, and workflow abilities. So i need to stay with taxonomy.

I want to have categories (vocab/terms) and have a content page for each category and then links in the menus for those pages below it. is this really that difficult?

any advice would be helpful.

thanks.