After reading this thread a bit I've become even more aware of the problems with these DVDs.
For example, the luma levels vary. Encounter at Farpoint is pretty good, with black usually being black. But I was watching Unification last night and black was consistently grey.
And there are really some very poorly transferred effects shots with what looks like black combing that's built into the frames and bounces around. DS9 and Voyager don't have this issue.
I've also noticed that some of the effects shots seem to be a strange/screwed up combination of telecined 24fps material and 30fps interlaced video.