The 2 episode DVD version of The Doomsday Machine was missing the music where Kirk "intends to ram her right down that thing's throat." It was restored for all later issues.
In the Laser/VHS verison where Scotty suggests they check the duplicate captain's log, there's a one second silence just after the cue starts. This was fixed for the DVDs. Beyond that, and other than what I pointed out previously, the music is intact on the DVDs and Blu-Rays.