Before the final test during the training of Bruce, Ra's Al Ghul gives him a bowl containing blue flower and some other things to smell in.
After that, Bruce faces his fears such as bats and death of his parents. But here he is able to control himself and fight.
However, when Dr. Crane releases the toxin, Bruce wasn't able to control his fear and got knocked out for two days.
Later, Ra's Al Ghul reveals that the toxin was made out of that blue flower and it appeared that Bruce had the same effect both times.
So, why Bruce was able to control his fear during training, but not when Dr. Crane attacks? Is there something more in the toxin?