ANOTHER UPDATE: Channing, Emerson, Parker, and Anthology!
Well, hopefully this update will make many lives a bit easier. All of my themes/flavors now auto generate their page links. So, the hard-coded page links in your header.php file will not 404 if you are using a different permalink structure than the theme assumed by default. In other words, your page links will work now! Hooray!
Thanks for all your patience. Update your themes if you are using Channing, Parker, Emerson, or Anthology! They now work if installed in a subdirectory, and auto-generate pages to deal with different permalink structures. These themes are seriously evolving! Thanks & Peace.