Currently, all the master copies of the episodes from the original run are being held by the Rock & Roll Hall of Fame. They were donated by Tad Low, the creator of the show. Although master copies are known to exist, they are not publicly available due to licensing. […] With the sheer number of episodes produced, the fact that both runs of the show are no longer rerun on VH1 or MTV Classic, and the fact that the show did not receive many home media releases (apart from a 1999 80’s-themed VHS / DVD) due to licensing issues, episodes of the show are very hard to come by. The only way that episodes can be found is through home recordings of the show from when it aired.
Music has caused a ton of licensing issues over the years. They’d license the music for airing on television, but not for sale. Or the licenses might have been format-specific.
Some shows actually have to do a second post-production phase for streaming so they can change the music. The first half of Scrubs has different music on the DVDs than they do on streaming because the licensing for the songs was specific to broadcast and DVD.