It seems that when parsing markdown files, GitHub flavour language specific code blocks aren't parsed correctly.
This is a problem for us over at CocoaPods (see CocoaPods/CocoaPods#289). We're happy to work around it if necessary, but we thought it would be worth seeing if you had any objections to us fixing the issue in appledoc, as it's a cleaner solution.
I'd be happy to implement this if you would be happy for the change to be made.
Thanks :)