Obviously no one involved is talking, so it's pure conjecture. Iran had previously captured intact drones though, so it's possible they were able to pull out the keys. Or it's possible that the public GPS was used after a period of having the encrypted GPS jammed (that's the kind of behavior that will never be confirmed).

Finally, it could have just been BS that GPS was what went wrong. That's not a bad guess.

http://www.wired.com/dangerroom/2011/12/iran-drone-hack-gps/