Buidling your site locally is the best way to figure out why it’s not publishing correctly via GitHub.
You must set up your gemfile specifically for each theme.
then prepare bundler for your project:
bundle update bundle install
Build gives an error message if the build fails
bundle exec jekyll build
Serve builds and “serves” a local browsable copy
bundle exec jekyll serve
Trace gives details on errors (but won’t always show your problem)
bundle exec jekyll build --trace
Verbose… you get the idea.
bundle exec jekyll build --verbose
Not sure how much of this is useful, but I’ll save for further examination.