The solution to bunny-hoppers is to follow them for a lap or two to see what's the fast line they use. Then on the next (and subsequent) lap get to the obstacle first, make a clean, fast dismount and then shoulder the bike cross-ways behind you as you run "their" line. If you time this right, the hoppus interruptus can result in everything from a determination to drop the hell out of you when he gets back on the bike to "Hilarity Ensues."
Of course the key is "get to the obstacle first make a clean, fast dismount." That's what's going to matter.