You're not the first one having trouble with DuckDNS, see also Propogation time limit exceeded. Seems like the nameservers from DuckDNS are often not responding or just way too slow. There's nothing Let's Encrypt can do about malfunctioning third party DNS servers I'm afraid.
Is there a specific reason why you're using the --dns-01 challenge by the way?
Also:
Please don't use this option. Also, please don't use options you don't understand to begin with.