I can't answer the question about why your TV looks worse now that the HD DVR is hooked up, but the answer to your question about "Why are there black bars on HD broadcasts?" is because the commercials either did not originate as HD material or if they were, the Ad Agency decided to make the commercial compatible with 4:3 TVs as well as HD TVs. You see black bars, but you see the entire image. If the commercial was in an HD format of 16:9, it would fill your TV but on a 4:3 TV the image would be cut off on both the left and right side. On HDNET, all their product is 16:9, so you won't see black bars. On local TV stations that broadcast in HD, they still need to cater to the old 4:3 aspect ration, which most TVs still have.
I have a 67 inch Samsung DLP tv. My cable co. came today and switched out my DVR to a HD one. My HD looks great but my other channels look really bad. A lot worse than they did b4 i switched out the DVR. Also, why are there black sidebars during commercials of HD broadcasts?