Menu Toggle problems with Nvidia Shield Controller

I have a 2017 Nvidia Shield and the latest stable 64 bit RetroArch (1.14.0). I have a Shield Game Controller and the Shield Remote. I start RetroArch and load the Fire Burn Neo core. The controller is recognized (set as Port 1) and the mapping looks to be correct. However in the Hotkey section I notice the Menu Toggle is auto set to the Nvidia Button. I have looked at the auto config file for this controller and it is indeed set to the Nvidia Button. But while playing a ROM, if I press the Nvidia Button on the Shield Controller, it launches the Shield Voice Search and does not exit to the RetroArch menu. It is like the button press is being sent to the Shield and not RetroArch.

So I manually set the Menu Toggle (Controller Combo) to L3 + R3. This works and brings me to the RetroArch menu while playing a ROM, but the Game Controller stops working at that point. I have to press a button on the Shield Remote, and then the Game Controller will start working. Often (but not always), when I resume the game, the Game Controller will not work until I press a button on the Shield Remote, then it will start working.

Any idea what could be causing these issues?