Jason never asks Bruce "Was I that unimportant to you?" After all, he doesn't know about the Fragile Memorial Case. But it is in everything he does in UNDER THE HOOD. The idea Batman never killed the Joker adds to the idea "Is HE somehow more important to you than ME?"
And I still believe Lazarus Pit Crazy Juice has something to do with it, as Ra's Al Ghul was using it AT THE SAME TIME she tossed Jason in it. And Ra's Al Ghul has his own set of "old school" morals.