A poster over at Blu-ray.com has noticed a new problem with the DD 2.0 audio on "Encounter at Farpoint."
I just checked my discs as well and I can essentially corroborate what he's saying. The DD 2.0 track of "Encounter at Farpoint" is stereo, but no longer encoded for Dolby Surround, and thus the various Dolby Pro Logic decode settings (PL, PLII, PLIIX, etc.) do not function. "The Naked Now" is also affected, but it appears that it NEVER WAS encoded for Dolby Surround, as "The Naked Now" on my original disc one also has non-existent surround information... or at least it is incredibly faint. When I disconnect my center channel speaker, I can just barely hear sound coming from the other speakers... but I have to put my ear directly against the speaker to hear it -- so as far as I'm concerned, it's non-existent.
"Farpoint" was fine on the original disc one (except for the delay issue!)... but now it seems after trying to correct the delay issues, they caused another problem.
So again, hang onto the Next Level sampler disc, as it still contains the definitive version of the pilot.