I had a problem last night with really bad reception on an OTA channel. It was WFMY. I have 2 antennas and a separate hdhomerun and lineup for each. I determined that the live feed was coming from the wrong tuner. I was able to fix it by changing the tuner priority and putting the correct tuner, for this channel, first.
I tried again this morning and it appears that the app on my shield tv is pulling all my stations from whichever tuner is first in the priority list. I submitted logs through the shieldtv.