I watched Encounter at Farpoint and Naked Now last night and didn't notice the audio issues (Of course like I said, I don't have a surround sound set up so I'm just using the TV speakers) but I thought I noticed some mumbling during the special features. I thought it was part of the gag reel and it meant to be there so I thought nothing of it. If they do have a recall, I'll take advantage of it, but reading some of these issues from people (And what I perceive to be slight overreactions) is disappointing to say the least.
After watching Naked Now though, I was really hoping the HD would actually fix the "Picard shouldn't have been infected because grunting doesn't intoxicate you" rule break that has bugged me for the longest time. Alas, it was not to be.