%80 of the day pi-hole works just fine. (I can access duckdns.org in a browser)
%20 of the day for no reason apparent to me, duckdns.org does not resolve.
If I change my LAN connection DNS from pi-hole to 8.8.8.8 while this is happening, everything works again.
If I keep pi-hole as my DNS and just wait, duckdns.org will be accessible again in an hour or so with no acton from me.
I dont see anything related to denying duckdns.org in pi-hole query logs.
I have the same problem; however, some .duckdns.org websites stay always resolvable, while others become occasionally non-resolvable by pi-hole. This might be due to DNS caching though, as the ones that seem to stay always resolvable, are accessed every minute or so (a cloud server).