What exactly does this have to do with GitHub Flavored Markdown? Literally none of GitHub's extensions to Markdown[1] work in this editor...
The source code for the app is using the github-markdown[0] gem to render - so it seems strange that it isn't working.
[0]: https://github.com/github/markup
Edit: Ah, heres the problem: https://github.com/github/markup/issues/47 - the github-markdown gem doesn't support github-flavored markdown, they must use a different gem or branch on the site