A review of the "Signs and Portents" DVD set has been posted at tvshowsondvd.com, and it has some interesting comments about the video quality of the discs.
The complete review also has some images to back up this theory.
In almost every episode there were one or two scenes that looked extremely poor. I'm talking worse than VHS here, and they stand out like a sore thumb. I started paying attention to these scenes, and came to this conclusion: the prints for some scenes must have been damaged so badly that they couldn't be used, so they were forced to use footage from a tape source. Since the tape would have a 1.33:1 image, it must be blown up and cropped for the 1.78 aspect ratio. Starting with an footage from a tape is going to result in a poor image, but blowing it up is going to make it worse.
The complete review also has some images to back up this theory.