Two years after the release of the first and second season of Moonlighting on DVD, I've found the answer to a minor mystery: why the episode "The Lady in the Iron Mask" was released with the wrong score (an inappropriately bombastic theme for the veiled woman and bland music replacing the "William Tell Overture" in the big chase scene). I haven't seen this explained elsewhere, so in case anyone wants to know the answer:
Richard Lewis Warren, who had scored a couple of early episodes (and had scored Remington Steele) wrote a score for this episode. Glenn Caron didn't like it, so he asked Alf Clausen to write a new score. (Clausen composed the music for all subsequent episodes of the series.) Clausen's score was the one with the "William Tell Overture."
However, the first score remained in the vaults, and when the show was being remastered from the original elements, the rejected score was mistakenly used instead of the final one. So what we're hearing on the DVD is the score that the showrunner threw out.
Too bad Lion's Gate didn't include the correct version one one of the subsequent sets, but anyway, there's the answer.