Hi,
I had the same issue. Arduino box has been setup in a remote location and I was trying to access it from home using a VPN access.
VPN was ok, I was able to access the web interface and ssh the box but impossible to make "Arduino Software" able to upload sketches. The box was not displayed in the port list.
I installed Avahi on the remote router and made it listen and broadcast on all interface. This way, remotely my computer was able to discover it and after that "Arduino Software" found it.