Traefik dns challenge with duckdns

Works for me, docker-compose.yml:

version: '3.9'

services:
  traefik:
    image: traefik:v3.0
    ports:
      - 80:80
      - 443:443
    networks:
      - proxy
    volumes:
      - /var/run/docker.sock:/var/run/docker.sock:ro
      - letsencrypt:/letsencrypt
      #- /var/log:/var/log
    environment:
      - DUCKDNS_TOKEN=<token>
    command:
      - --api.dashboard=true
      - --log.level=DEBUG
      #- --log.filepath=/var/log/traefik.log
      - --accesslog=true
      #- --accesslog.filepath=/var/log/traefik-access.log
      - --providers.docker.network=proxy
      - --providers.docker.exposedByDefault=false
      - --entrypoints.web.address=:80
      - --entrypoints.web.http.redirections.entrypoint.to=websecure
      - --entryPoints.web.http.redirections.entrypoint.scheme=https
      - --entrypoints.websecure.address=:443
      - --entrypoints.websecure.asDefault=true
      - --entrypoints.websecure.http.tls.certresolver=myresolver
      - --certificatesresolvers.myresolver.acme.dnschallenge.provider=duckdns
      - --certificatesresolvers.myresolver.acme.dnschallenge.delaybeforecheck=20
      #- --certificatesresolvers.myresolver.acme.dnschallenge.resolvers=99.79.143.35:53,35.182.183.211:53
      - --certificatesresolvers.myresolver.acme.storage=/letsencrypt/acme.json
      - --certificatesresolvers.myresolver.acme.email=mail@example.com
      - --certificatesresolvers.myresolver.acme.storage=/letsencrypt/acme.json
    labels:
      - traefik.enable=true
      - traefik.http.routers.mydashboard.rule=Host(`traefik.duckdns.org`)
      - traefik.http.routers.mydashboard.service=api@internal
      - traefik.http.routers.mydashboard.middlewares=myauth
      - traefik.http.middlewares.myauth.basicauth.users=test:$$apr1$$H6uskkkW$$IgXLP6ewTrSuBkTrqE8wj/

  whoami:
    image: traefik/whoami:v1.8
    networks:
      - proxy
    labels:
      - traefik.enable=true
      - traefik.http.routers.mywhoami.rule=Host(`whoami.duckdns.org`)
      - traefik.http.services.mywhoami.loadbalancer.server.port=80

networks:
  proxy:
    name: proxy

volumes:
  letsencrypt:
    name: letsencrypt

When using Traefik v2 you have to remove entrypoints.websecure.asDefault.

Maybe setting the DNS IPs with the short delayBeforeCheck is the problem. Try removing the IPs and extending the time.