This started when I could not refresh a repo on my Linux installation. Doing a manual wget --spider on the metadata file that it could not retrieve revealed that it was trying to connect to the IPv6 address of the mirror site.
My Internet provider does offer a dual stack IP service but I have not activated the IPv6 portion yet. So the question was how to make sure any http/https clients prefer the IPv4 address.
A web search gave the answer, you edit the file /etc/gai.conf which controls the behaviour of the getaddrinfo(3) function. In it you will find a comment to uncomment the line:
precedence ::ffff:0:0/96 100
if you want IPv6 addresses to sort lower than IPv4 addresses. I also reloaded the nscd service to flush any cached entries.
I suspect I hit this problem because I run my own DNS resolver. If you are relying on a DNS relay from your Internet provider they may have filtered out IPv6 answers for the sake of compatibility.