I have a 60" Vizio tv M series from 2014 (1080p). When I hooked up my shield tv on it the TV remote got disabled and/or the TV became very slow to respond.
So I can't turn off the TV, change the volume, and change the input channel.
Pretty much the TV gets stuck to android tv.
I don't know what's going on!
On a side note: One of the most frustrating things about the network app remotes i.e. smartphone remote, android wear remote is the inability to control the volume or power the set on/off.
Can't really help your issue. I know that they are doing some fancy things with IR remotes based on whichever input is active. Maybe check your HDMI link settings.
Do you have the HDMI (CEC) settings on with 1 or both devices? It sounds like the HDMI link it trying to take control when it shouldn't. Also, be aware many TVs have per input settings now. Keep that in mind when digging through the menus. All else fails do a full reset on the TV. TVs are known for getting bugged out with some obscure settings