This thread is closed as LE works both on IPV4 and IPV6. The reason I opened the thread was because I had some routing issues with IPv6. In my understanding I was serving IPv6 as some IPv6 validation sites showed that it was ok. However the router (one that is not all that easy to configure) was blocking icmp packages for extra security reasons. So, LE was trying to validate the domain but failed. I must say that some bad things end up to be good because I went back and fixed the issues that was wrong that otherwise I probably would never find out that was wrong.
At first instance one would just turn-off IPv6 or start to blame somebody else. I did that, I was wrong and I admit that! Then I decide to take the challenge to fix the IPv6 routing by going back and fixing the issues. Now, things are working. Thanks everyone that participate on this thread.
So, just to summarizing;
The problem was not DNS mis-configuration but a router firewall configuration