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I have been creating a custom theme for my drupal website and I ran into this problem where the Drupal Administration Menu (module) disappears for custom themes that are not based on out-of-the-box themes. I did a lot of searching for a solution with no luck, so in the end I just ran through the code of existing themes to see what code is required for the menu. Hopefully I can help someone who may have the same question!
You basically need to have this code at the end of your page.tpl.php file: