Well, if Github nowadays runs on Azure under the hood (which they probably don't) I understand. IPv6 support in Azure is patchy with many of their services.
I think they run their own servers; a little bit of DNS poking, followed by a traceroute, led me to what I think is a colo company called Twelve99. This is just for my region; I imagine they run servers in different datacenters all over the place, and maybe have some sort of presence in AWS or one of the other public clouds.