How come they didn't use the original theme music from the films ?

Good question, often wondered that myself. They used the Raiders Theme in one episode however, "The Mystery of the Blues", but only in the scenes with Harrison Ford as 50 year old Indy.

Probably because the Raiders March is the musical theme of the adult Indy rather than the young Indy.

No, just kidding, actually they did it specifically to annoy and confuse you. Yes, you personally.

Yeah, I guess you're right. While I've grown to appreciate the "Young Indy" theme by Laurence Rosenthal, I definitely miss hearing John Williams' triumphant "Raiders" march. The only episode where it was used was "Young Indiana Jones and The Mystery of the Blues," at the beginning and end, during Harrison Ford's cameos.