Hmm, strange symptoms. I haven't any issues like this. I've been using github pages + CNAME + gh-pages as project pages together for over a year without any issues whatsoever. Didn't have to worry about submodules either. Not sure why you're into these issues, kecebongsoft. I've used Jekyll as well as plain old html. I'm sorry you've had issues like this but I wouldn't discourage people from trying it either.