Rights were only granted for the show on tv, and the occasional soundtrack. Those rights have to be renegotiated for dvd. The producers of Crossing Jordan are currently working through that very issue, they're hoping to release s1 sometime this year.

Some dvds are released with different music than the original broadcast. Northern Exposure and Scrubs are just two that have had that problem. Apparently some shows only have the rights to use certain songs in the original broadcast, so the music is different even when the show is repeated on tv.

It's apparently quite a complex area.