The agent image is also Ubuntu, so my guess would be your cert is signed by an intermediate cert that is not being sent. And that intermediate may happens to be in browser/Mac OS stores so it still validates there, but not be present in Ubuntu 14.04. You can go to a host and try:
docker run --entrypoint openssl rancher/agent:v0.11.0 s_client -CApath /etc/ssl/certs/ -connect rancher.myhost.com:443