Hi Swordfish,
I would un-install and delete, then try a fresh download of the auto and harbour scripts
If that does not work, can you look in the automation folder, as TDW said. A post a screenshot of the auto folder could help spot a problem.
There are some Auto scripts within TDWs UI. They should be showing up in the menu screen as in pic2 by Stoianm. Is there no items at all in that menu