I haven't used auto-bombard, so my answer is all hearsay gleaned from the forums (but hearsay that rings true to my ear nonetheless

). If you have checked the preference item "Wake when next to enemy unit" or its equivalent, that preference will override the auto-bombard -- the catapults, set to auto, "wake up" before the auto-move portion of the turn because they are next to an enemy unit. Seems a little silly, but there it is.
Catt