@gertjan
I was able to get it working thanks in part for your suggestion of checking the option “Enable DNS domain alias mode”.
The other part of the problem was that I typed the wrong CNAME information in my DNS provider.
I had:
_acme-challenge.cloud.MYDOMAIN.com --> MYDDNS.duckdns.org
The acme challenge Alias needs this CNAME to be
_acme-challenge.cloud.MYDOMAIN.com --> _acme-challenge.MYDDNS.duckdns.org
CNAME-corrected.jpg
After making these corrections ACME was able to issue a certificate for my domain as expected.
Thank you so much for the help.