When Get a Life re-ran on USA Network about 5 years ago, the music was changed in all the episodes, except for one. I forget which one, but it had a musical guest in it, and I guess they secured the rights to the music for that one single episode, and only that episode. Otherwise, the theme and in-show music was replaced and even the credits screen with the music was altered (which is odd, because the credits were single frame screens).
I have the 2 VHS releases from Rhino. Both have the original audio soundtracks in place. I never owned the DVDs though.