I can only speak to the music and sound issues in The Complete Collection.
Give Me Liberty or Give Me Death – Hurts So Good. Replaced with generic music. (The song is there in the Season 1 DVD set released in the early 2000's.)
White Line Warriors – Little Red Corvette. Replaced with generic music.
Dead of Knight – When Doves Cry. The song was just taken out and there's no music in the scene. (I have yet to see this episode be available in syndication. (At least where I live.) So it doesn't bother me as much. I'm just happy to have the episode at all.)
Knight of the Drones – Pretty sure the song was Little Red Corvette. Received the same treatment as Dead of Knight.
None of these changes ruin the scenes, though it's amusing to see people dancing to no music. Compared to the music changes other shows like Quantum Leap received, KR got off lucky.
Most of the audio issues that were in the first set of DVD releases were fixed in The Complete Collection. The only one that really stands out to me is the sound of the boat's engine in Knight of the Juggernaut.
Just me personally? I think buying the KR Complete Collection is one of the best fandom investments I ever made. It has just about everything that I was looking for. Maybe the Blu ray set has bells and whistles and improved content and visuals that other fans are looking for as well, and to them it makes up for any missing music. Nothing wrong with that, but I'm more than content with the set that I currently own. It comes down to personal preference.
Hopefully those who own both will be able to answer which is better and what issues the new one has. Good luck!

If you'd be so kind as to put me down.
Down?
My dear, I'm a car. Not a plane.