Tim Witt,
OK here is what I found. By default Github pages do not publish files with certain file name structures. I found this document to explain and give a work around.
Files that start with an underscore are missing - User Documentation
I don't really know what jekyll is, but I put in a .nojekyll file (the .nojekyll file is blank) in the root of the repository. I added it to the gh-pages branch too but for some reason it did not take. I deleted the gh-pages branch and recreated it and it looks to be working now.
-Stan