If you want to control the Shield over Bluetooth instead of IR, add it as an Asus Nexus Player. Works great!
(Use the mobile app to set it up. During setup, where it says to hit the button on the bottom of the Nexus Player, instead go to Settings -> Remote & accessories -> Add accessory.)
It never says to press the button on the Nexus Player. Are you using the MyHarmony app? I cant figure out how to get the BT to pair.
Also, there is a Nvidia Game Console in the database. I tried it too and was not prompted to pair.
[Edit] I got it to work with the Android app. The stupid desktop software doesn't support bluetooth pairing. But the typically shitty Logitech software doesn't tell you this.