The Docker images have changed slightly with the new build method. The correct path is now:
/opt/duplicati/duplicati-server
The Docker images do have this as the entry point, but in case you have provided your own entry point, this would explain it.
You need to go all the way back to 2.0.8.1 to get the /usr/bin path. There was a slight bug in the deployment of 2.1.0.2 that did not publish the latest tag on Dockerhub, but 2.1.0.3 is published as latest now.