How Windows handles the controller GUIDs are a little chaotic sometimes. My initial suggestion is to try a reboot of your PC to see if your controller defaults to Player 1. If I let my controller's bluetooth time out, and I reconnect it again, for some reason the USB slot increases (player 1 become player 2 and player 2 becomes player 3, etc)...its pretty random...in my case, all I need to do is a reboot of my PC to set everything back originally. If that doesn't work, you can use a nifty program called usbdeview to help assist in your troubleshooting and potentially remove old devices. BTW, what emulators are detecting your controller as player 2?
In my set up, I actually use a bluetooth adapter and connect a DS4 controller to it instead of connecting to the Shield's bluetooth. Steam is not installed on my Shield or PC....I just rely on nVidia's gamestream service to stream my desktop. When I connect to my Windows PC without a controller and open up device manager, I see a Xbox360 Controller for Windows thats mapped to the Shield (has location NVVHCI Enumerator within its properties....dont disable/uninstall this or your Shield may not connected back up to your PC). When I connect my DS4 controller via bluetooth, I see another instance of Xbox360 Controller for Windows thats mapped to SCP Virtual (its the virtualhere driver).
As far as renaming the rxgamepadinput.dll, I renamed not only this file, but the rxgamepadremapping.dll and rxnvgamepad.dll. There are two locations where these files reside (Program Files and Program Files x86). I believe this just disables the nVidia controller from connecting in your stream session I believe. You will need to reboot after renaming the file(s).
Hope this helps!