I'd like to add a couple things on this topic:
First, I've noticed on one show that there was a delay following commercials for the DD to kick back in. Not sure if it's the feed or my box, and it doesn't happen all the time.
Now the issue of the levels.
There is a noticeable difference in levels, but to me that's OK. What I don't like is that the audio doesn't seem to be mixed in true 5.1 DD. I can barely hear my subwoofer which usually helps to round out the dialogue and kicks in during musical passages. So what I think is going on is that the original audio track is merely mixed in stereo and then from there it's faked into a 5.1 environment - sorta like Dolby Prologic.
If this is the case, then the sound engineers for the program don't have to supply two seperate mixes for the show - but they're defaulting to the lowest common denomiator, and robbing us of the full experience. (Not unlike using the same title menus for both SD and HD programming)