I think it's a known issue, for some reason only level 1 casting time is used..
A work around could be making a second ability that works like the level 3 of your ability, but with the desired casting time on all 3 levels. Then with a trigger, when the hero learns level 3 of the normal ability, you remove the original spell and put the second one. It should work.
Be wary though that resetting the level of abilities with triggers or items could lead into undesired situations, which can be fixed with more triggering anyway.
EDIT: I couldn't find any fix for this problem so the above mentioned substitution trigger seems to be the only solution