Murph,
The scene you described on the 5th episode of DS disc 5, with the Reverend and Ben, in which the scene breaks up and goes to black. That is actually not a flaw of the DVD transfer. This is one of the many damaged pieces of video footage that plagues many of the original episodes of DS. It is that way on the original master tape. You will see many of these "black" break ups in future episodes. The reason you don't see it on the syndicated episodes on sci fi, is because Worldvision went to great pains to remove those "flaws" from all the shows currently airing on sci fi. I described Worldvision's "tweaking" of the sci fi tapes in a past posting. This was done to make the show more broadcast quality. Over the years, these tapes have been damaged due to mishandling or poor storage conditions.
Wait until you see episode 479 on DVD. On the original master tape, there is an actual break in the tape in the scene where Barnabas is trying to stop Dr. Lang from cutting off Jeff's head. Missing in that scene is about 30 seconds of video. On the sci fi channel tape, Worldvision cleverly edited this scene so you don't see the break in the tape. I know this because I have an original 1968 audio tape of the episode, which contains the missing 40 seconds of video.