There's a hidden menu on the newer Fios boxes where you can enable additional output resolutions and/or force the box to output the native resolution for a given channel.
To access it:
-Have your tv and set top box ON
-Then use one hand to power OFF the STB, and the other hand on the remote and hit OK once and then menu once (do them about 1/2 second apart) - so power 1/2 second OK 1/2 second menu
-Once you're in then you click on additional HDMI options and the video settings are in there