I'm having the very same issue, which began only within the last week or so, affecting both a Roku Select 43" set and a TCL 55". In this case, we use an HDMI-over-Cat6 distribution system to feed video from a computer to multiple Roku TVs. To save electricity, the distribution box is only powered on when being actively used, but once it comes online, suddenly everyone gets bothered by the same useless pop-up box others here have mentioned, despite the input having already been set up and labeled (and re-labeling it over again never helps).
Beyond fixing this recent regression, it would be nice to also have a menu option buried in settings to disable the "auto detect new inputs" feature altogether. That way, there would be no need to clutter the tiles list with rarely-used inputs; a video-source computer or other automation could send an ECP command to switch a TV over to its feed (e.g. POST to http://my.roku.tv.ip:8060/keypress/InputHDMI4). Maybe there wouldn't be much demand considering the specialized use case, but such an option could also be an easy mitigation for this phantom pop-up issue, until its root cause can be identified. Default the auto-prompt to on as now, but I'd imagine most here could live without it for a while.
