After troubleshooting this with Comcast, Sony, and Samsung, I have narrowed this issue down to just one problem. It took some time, but this is the only issue I am having with this STB.
Here is the issue: When I change the receiver to FM Tuner to listen to the radio and I turn the Samsung off and the Motorola STB off, the Motorola flashes DVI (or maybe DUI). It is at that moment when it flashes DVI, the STB reverts from 1080i to 720p automatically. This 720p setting (with 4:3 override changed to off) is the default setting with this STB. The audio settings that I selected (Pass Though) are also reset to Auto, which is the default audio setting. In essence, the STB is changed to default factory settings when I listen to the radio.
It is my opinion, that when switching the Sony to FM Tuner, the HDMI/HDCP handshake is terminated or interrupted and this reverts the STB back to 720p and tells the STB to go back to default settings. The default settings on this STB are 16:9, 720p, 4:3 override off.
I think Motorola should come out with a firmware upgrade that will force this STB to always stay on the user selected settings, versus going back to default settings. My older HDMI/DVI STB never changed its settings.