On the back of the case, it says in very small text: Music has been changed for this home entertainment version. That is partially correct. I saw a few scenes where the original music had been replaced with either instrumental music or another song. I did notice at least 2 scenes that were omitted entirely on the DVD....
In the "Pilot" episode, there is a 30 second scene (accounting for the 23:31 running time on the DVD vs. 24:01 on the tape) that was cut entirely. The scene has Steven and Elyse relaxing in the family room, and Alex comes in and says the ambience is all wrong and he turns off the stereo, which was playing the folk song "Days of Decision" by Phil Ochs. It seems like they could have just replaced this song instead of editing the scene entirely out.
In the third episode, "I Know Jennifer's Boyfriend," there is one scene that was entirely cut out and at least 3 songs that were replaced. A 30 second scene of Steven and Elyse singing "Eddie, My Love" by The Teen Queens was cut out entirely. If they couldn't get the music licensing rights for this song, I could understand why it had to be cut.
Three songs at the 1950s themed party were replaced. There were tiny clips of "Wake Up Little Susie" by The Everly Brothers and "Earth Angel" by Chuck Berry that were replaced. Elvis Presley's "The Twelth of Never" was originally used for the closing dance scene, but it was replaced on the DVD with some modern sounding song that really didn't fit the 1950s party theme or the scene nearly as well.
I can understand replacing some songs if they're too expensive, but it sounds like Paramount just replaced anything music-related and, if the scene didn't work without music, they just cut the scene. This does not bode well for future seasons (the "A, My Name is Alex" episode used "Light My Fire" by The Doors"), and it seems kind of shabby.
Of course, every show that turns up on DVD now makes you worry a bit as to what music made the cut and what didn't. But you kind of expect that they'll leave something in there.