Got an answer from GitHub.
Thanks for contacting GitHub Support, and apologies for the delayed reply.
To confirm, are you referring to this repository?
If so, it looks like the cause of the trouble you described was that the repository’s custom domain settings were repeatedly being cleared by a CI tool. If you take a look at the commit history for the gh-pages branch, you’ll see numerous instances of shadowislord creating a CNAME file (which enables a custom domain):
And then, shortly after, Travis CI deleting the CNAME file (which disables it):
To resolve this issue, you may want to look into your Travis CI configuration. I can, however, assure you that nothing is wrong with the GitHub Pages service itself.
I hope that helps! Let us know if you have any more questions.