Enemies will sometimes refuse to make the jump if they would take damage doing it. Have you tried swapping the Hunter for a different NPC and see if they jump as expected?
I've successfully had Hunters jump down from 128 tall ledges in the past. Are we talking about a Fast Zombie jumping from roof-to-roof scenario here, or something more basic? I have my doubts that one could get too exotic with Hunters, given that Valve wound up doing a lot of canned animations for their appearances at the start of Ep2.