The story behind the song Jimmy James is told in the liner notes of the Beastie Boys compilation, The Sounds Of Science: In homage to the great Jimi Hendrix, MCA had scratched a number of Hendrix samples into the song, but the record label was unable to obtain clearance for those samples before the Check Your Head album was ready for release, so they had to be replaced with others that sounded similar.
Meanwhile, after the album was finished, the Hendrix estate finally granted permission to use the original samples, so the Beasties put out the "OG version" as a single, and on the Best Of set. (And a good thing, too, because the Hendrixified version sounds much nicer.)