TVShowsOnDVD.com had a news item about this, back around thanksgiving time. The basic gist of it was that the reason season 2 was taking so long had mainly to do with music rights issues, Fox was more than eager to get this one on the market, but it hasn't been easy clearing up songs. I don't know what the status of it is now though, but I'm thinking that's what I read back in late November.
Agreed. I really can't remember any big music that would be holding this up. I assume that the rights to the TMBG music is already cleared since it is on S1.