there are a number of episodes that have weird music changes, added cues and such.
Which episodes in particular? The only music changes I know of are during The Menagerie, Part II. That episode's DVD [Region 2, both original and remastered] version uses a re-recorded cue in the opening fly by shot, and again later in the episode. After the opening titles, during the episode titles/Capt's Log, a cue from The Doomsday Machine replaces The Enemy Within. Also, the truncated Max's Factor cue when Vina is returned to beauty is slightly modified on the DVDs.
I also *think* some of the instruments from Kaplan's Doomsday Machine are added into some of The Enemy Within Enterprise cues.
Other than that, I'm not sure...