I own the Shield TV 16GB 2nd Gen and the Shield TV Pro 2nd Gen (I'm not using the Flirc with the Pro as it has a built-in IR receiver). I struggled for some time to properly set up the Flirc and Harmony 650 but have found a solution that has worked for me.
This is what works for me:
Run the MyHarmony app.
Add the device:
Manufacturer: Nvidia
Model: Shield
The MyHarmony app will ask if it is the NVIDIA SHIELD TV. Tell it "Yes" and you should see a full array of options for the buttons.
Program the MyHarmony remote's activities and buttons as desired.
Adjust the Shield TV's "start" activity to include:
Shield TV Home command
Adjust the Shield TV's "stop" activity to include:
Shield TV Back command
Shield TV Home command
Run the Flirc program in connect the Flirc to be programmed.
Under "Controllers" select NVIDIA Shield:
Program each of the functions.
Under "Controllers" select Kodi:
Program all functions other than the Shield functions programmed earlier.