There are four types of music licensing and royalties contracts at work here.
Master Use - Use an existing recording that someone else made. To my original point, above, U2 owns its master tapes catalog, so Paramount undoubtedly pays U2 for non-live recordings placed in the film, ie, AllI Want Is You. The rehearsal footage from Sun Studios, likely belongs to U2, too, because it was caught on audio tape during the recording and mixing of the final original song written and performed by U2. (As an aside, the Memphis Horns, for example, are union members and would have received a flat hourly or negotiated fee to be and perform in studio. They would not receive any royalties unless they were credited with writing/composing the original song.).
Synchronization - Record a song that someone else wrote and put it to video. Because U2 wrote and performed the song, Paramount pays U2 to "synch" the music to the film and distribute it.
Some sort of Mechanical license was required to reproduce the film on VHS/DVD, etc.
Public Performance - Perform in public a song that someone else wrote. U2 likely paid the royalty for All Along The Watchtower.
And since Jimi Hendrix's performance of The Star Spangled Banner (public domain) was played over the PA system, U2 should have paid a license fee to "broadcast" the song and a synch license to use the other artist's master recording in conjunction with the film and record.
Sterling Magee and Adam Gussow would have also received several contracts for the perpetual use of Freedom For My People. Unless U2 bought the rights and publishing, they also receive royalties for the song too, each time it's played in a theater (cue sheets) or broadcast on radio or TV.
Paramount financed (produced) the film and probably retains the distribution rights. This question could probably be answered in the liner notes of the GH vol 2 DVD. If One Tree Hill is "courtesy of Patamount Pictures (Viacom)", then U2 pays the film company for use of the images.
Ok, back to work.
Lance A Schart
Chicago, IL USA