Ok, now i moved from my VM to a Raspberry pi 3. And get the same behavior. Without bluegiga all serial ports are shown in zwave binding. The after installing the blugiga binding only one port is show, but this port ist not the zwave port. Uninstalling bluegiga does not change anything, but after a restart all ports ar shown for zwave.
So i would say that that has definitly has nothing to do with a VM 
by the way i do not use ESX for virtualisation i use the Synology virtualisation