I tried the suggestion from AlGriefer above and that doesn't work on my Bose Lifestyle V20 (I bought on Saturday) and my Logitech Harmony 890. In fact none of the suggestions above seem to work. I spoke to Bose for about 20 minutes since my Bose remote wasn't always turning my TV off on system shut down and I have to turn on the HD Cable box on separately when I pressed the Cable/SAT button.
Nothing we tried worked, he suggested I call Support on Monday when this 'one guy' would be in and he has V20 and Logitech remote an has them working at home.......

And there is definitely something wrong with the remote, the IR and the software on the Bose.

I also get picture clipping when i'm in Menu mode. Everything is connected HDMI and secure. Bose support had no suggestions.

Stay tuned.