[curt_gendron]

It is probably your TV getting stupid when changing inputs. Can you send the audio to the Bose system through a optical cable? Or even try an analog cable to see if that makes a difference.

Does you Bose system have a digital pass through like a receiver has? In other words the ability to have all the TV signals go to it and pass the TV signal to the TV and the audio out to the speakers. Then that would be doing the "switching" instead of your TV.