I also have the same issue on Windows 10. Two xbox one XINPUT controllers are both showing the same IDs. Here is what my settings.ini looks like...
[Game Ports]
Port1=VID_045E&PID_02FF&IG_00
Port2=VID_045E&PID_02FF&IG_00
[Daemon Settings]
DaemonMode=FALSE
DaemonModeDelay=10
When i reboot it will actually disconnect my controllers and will not reconnect them