Drupal Coding - Menus - hook_menu is not generating menus
The place to start debugging is in _menu_navigation_links_rebuild() which builds up the menu links...it gets passed the menu router items built up from menu_router_build() (which is where hook_menu() is called from). A bit of temporary debug code in that first function would be the best way to go I think.

To address your other question, I've just added a menu item to a module in exactly the way you've done and it's come up in the UI as expected. It sounds like you have something pretty unusual happening with your menus!