This is by design - Docker for Windows works differently than docker-machine. With Docker for Windows installed, we recommend using docker-machine only for remote machine creation
Basically, docker-machine expects the machine to be available through ssh which is not the case with the VM within docker for windows.
See Should MobyLinux appear in the results from "docker-machine ls" and "docker-machine ls" doesn't show MobyLinuxVM...is this correct?