The message I get is "You have to use the Harmony App to pair this device." And like I said, the bluetooth connectivity is working just fine for the nvidia shield commands, but for the windows pc keyboard it shows that message every time.
Update: I've made a new activity with all the devices in there. That didn't change anything. I have removed the harmony device from the shield and re-paired multiple times, and that hasn't changed anything. I have compared all my settings to a second Harmony setup I have in my family room, which oddly enough seems to work fine. The difference there being that the family room system uses a Smart remote instead of the Ultimate. Not that it really should make any difference in this case.
Also, the soft keyboard in the app does work to send keystrokes to kodi. Now if only Harmony would let me assign those keystrokes to a button on the remote I'd be all set. But as it is I can only use Windows PC, and that just doesn't work.
About the only thing left that I can think of is to remove the Shield and PC devices from the harmony altogether, as well as the activities, and start from scratch.
Update 2: And apparently this is all Logitech's fault and it's broken other people's systems. I found this
thread and it seems to be identical to my issue. Unfortunately following the steps there hasn't helped me out one bit. No matter how many times I remove the device, activity, paring, etc., I get the exact same results.