If it's strictly a player problem, why is it JUST Season 2 of Star Trek? Season 1 doesn't do it. Other blurays with different audio tracks don't do it. Maybe CBS mastered the disc oddly so that some players don't play them property but some do.
I see some poor decisions in other aspects of the Star Trek bluray:
No scene by scene access. If you want a resume in the middle of an episode, you must start at the beginning of the episode and fast forward, instead of pressing "next" a few times. I can't think offhand of another bluray or DVD release of ANY TV show or movie that cheaps out to this degree.
The bluray does not save where you were last watching if you turn player off in the middle of an episode. On every other bluray or DVD I've played on my player, if you turn the player off in the middle of a show, when you turn it on again it resumes where you left off.
Same with the settings for audio track and subtitles. On every other bluray, if you set subtitles on and a particular audio track, then turn the player off mid-show, when you turn it back on those settings remain. Not Star Trek.
And the intro splash screen is set to be unskippable and un-fast-forwardable. I know the lawyers told them the copyright notice had to be unskippable, but on most discs the various logos and animations can be either skipped or fast forwarded. This is not a unique issue for Star Trek, but it combines with the other issues that are unique to Star Trek discs to waste several minutes every time you start watching it. They should have a little humility about their animated control screen, once I've seen it once, I don't need to see it again, I just want to chose my episode. Most discs respect that and put the episodes on the main menu for the disc.
Thinking of selling the bluray set and seeing if I can get the DVD set.