I did a decent amount of searching for this issue, and the most I was able to find was a thread form about a year ago where several people had a similar issue, but no solution.
I have a Dynex DX-37L200A12 TV and a Motorola 2500 cable box (Verizon FIOS). I've run into an issue trying to get my new Wii U set up to control both my TV and my cable box. When I go through the TV set up, and set up only the TV, everything works fine. Volume, channels, and, most importantly, switching inputs. However, when I set up the Wii U controller to control both the cable box and the TV, I lose the ability to change inputs on my TV. When it is set up for the TV exclusively, I switch inputs by tapping the Input button on the remote, navigating up and down on the list with the d-pad, and selecting the correct input with A. When it is set up for both, I am no longer able to do this. The d-pad does not cycle through the available inputs, and tapping the input button again only makes the input screen go away. I have gone through with all 5 Dynex signals, and as many as the Motorola ones as I could, and no combination makes this work. From the limited information I was able to find, it seems that this occurs because when the Wii U is set up to control both the cable box and the TV, it assigns the d-pad and other buttons to navigating the menus on the cable box, leaving any navigation required on the TV unusable.
Does anyone know of any possible solution to this? Given that the only posts I found were from about a year ago, I'm guessing either there was some official fix I missed or people just gave up on a fix or patch any time in the near future. Still, I'd appreciate any help or suggestions anyone may have.