The reason: too many people in the credits.
Apparently, the Academy in their infinite wisdom think that only one or two people should be credited as a composer or collaborator on any one piece of music. The list of composers on the Dark Knight score lists five.
In a previous interview with Variety, composer Hans Zimmer stated that listing the other collaborators on the music cue sheet - the official document that ASCAP and BMI use to distribute royalties - was a way of "financially rewarding" the other team members who helped create the music.
Variety states that the music team jumped through several hoops to get the music nominated:
Zimmer, [collaborator James Newton] Howard and the other three individuals -- music editor Alex Gibson, ambient music designer Mel Wesson and composer Lorne Balfe -- reportedly signed an affidavit stating that the score was primarily the work of Zimmer and Howard.
That apparently wasn't enough for the majority of the committee, which was also supplied with documentation indicating that more than 60%, but less than 70%, of the score was credited to Zimmer and Howard.
The same problem happened to the score for "Batman Begins" in 2005.
Stupid. Stupid. Stupid.