According to this latest Huffington Post article reporting on a recent interview of Colbert, it would seem that it was possibly Daft Punk that cancelled their highly anticipated appearance on the show:
"Colbert says that he still was unsure why exactly the cancelation occurred. "MTV says they had an exclusive arrangement, Daft Punk says they don't have an exclusive arrangement," he told Mecurio. This corresponds with MTV's official statement, which was that the cancelation was the choice of the band, not the network."
Read the full article on the Huffington Post.