This might have been discussed but I think it should be shared again as it took me 2hrs to figure out a fix.
I have an Harmony hub that worked perfect with my Nexus Player.
Just upgraded to Nvidia shield TV 16Gb Gen2. Therefore, no IR btw.
When I added Nvidia Shield TV to my list of devices, the back button on my remote did not work. A few other "glitches" too.
The fix was simple: in Harmony when using the Hub, pretend your Shield TV is a Nexus Player. It will pair over Bluetooth and all the buttons will be fixed.
I had to re map buttons for my gen 1 Shield to work properly with my Harmony Hub. They always defaulted to TV control. After setting it up as a Nexus Player, everything is working better than before. The Bluetooth control is smoother than IR. I can now hold down on the directional pad of the remote to scroll through menus instead of tapping multiple times. Thanks for the tip.