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I'm having problems with it too. I plugged in the new IP addresses for my root A records yesterday, and then deleted and re-added the CNAME file in the repository. GitHub support said they manually started the certificate provisioning process several hours ago, but I'm still getting certificate errors.

You may not have had a certificate issued for your domain yet. The steps I went through for this were changing the CNAME, which made GitHub go try to get a new certificate for me.

It issued a certificate for the www subdomain which is working fine. I need it to issue one for the root domain too.

I was having trouble with that yesterday, as well. On the settings page for my repository, I switched from www.example.com to example.com and then back again to www.example.com. I noticed it is now working for my site, though I don't know for sure that my changes fixed it.

https://help.github.com/articles/troubleshooting-custom-doma...