Transposons are supposed to jump in and out of DNA. And usually everything goes OK.
Sometimes they get left behind in the host genome because the transposon loses a chunk of something important (and it can't move anymore).
McClintock's maize transposons suppressed a color gene (I don't know how -- probably because it was sitting in the gene). If the transposon jumped, the gene suppression disappeared and the maize started making pigment.
So, technically, those transposons weren't junk DNA (cause they still worked).
Edited by molbiogirl, : No reason given.