The lack of control the content providers are giving is disheartening. It creates no end of problems for HDTV makers as you see this.
The fact the same channel works on the commercials is telling us something is amiss with the HD audio. Commercials are often stereo and 5.1 is something else.
There's another item to consider such as hookup. Your better HD tech will never run audio out of the TV to the HT system except for OTA and maybe game consoles. Be sure you hook up Source->HT-HDTV.