Addons need to be "registered" with the updater before the updater will track them. This is so it doesn't go out trying to update an addon that WoWInterface does not have, and then overwrite it with an outdated version, or worse, something that is completely different.

To register an addon, go to the "file" menu at the top of the window and choose "register." From there, select the addons you wish to register, and press the ">>" button. This will move them into the registered list. Once you hit OK, the updater will perform the first pass on these addons (see "It's updating everything, even addons that are already up-to-date!")