I have noticed a rather disturbing matrix encoding problem with the surround sound of episode # 12 of season 2:
The center channel and the right front channel are flopped / reversed, i.e. the dialogue does not come from the center but from the right speaker.
Vice versa, the music and ambient sound effects come from the center speaker.
This is extremely annoying - To properly watch the episode I had to switch the speaker cables 
This problem has been observed with the European PAL version of the second box set of season 2. This is a rather unusual defect that usually would require Paramount Home Entertainment to fix the problem, repress this DVD and offer a free-of-charge replacement.
Unfortunately, it seems impossible to get a reply from Paramount Home Entertainment Germany or ANY e-mail address of Paramount Home Entertainment UK (the DVDs here are pan-European, i.e. DVDs are the same all over the place).
I can only urge those in the UK or elsewhere in Europe to check the sound of their DVDs. There is a certain probability that the same problem occurs with the NTSC DVDs, but that needs verification.
(and while the picture quality of season 1 and 2 is excellent by all means, the pilot episode is of somewhat inferior quality. I hope for the ultimate DVD release that not only the box cover is changed but that they find the original negatives of the pilot episode and remaster it...).
Have a better one!