Having a handful of burned out plugs will cause it to cycle rapidly like that. The controller senses resistance in the circuit. Normally resistance increases as they heat up , usualy at around 12-15 seconds, but when plugs get old and worn, resistance increases sooner till the controller will cycle on and off from the moment you trigger it. if you bypass it, you may be feeding juice directly to old plugs and could risk burning some tips off.
Before you go nuts and start bypassing anything, get a meter out and yonk the leads off you glow plugs and test the resistance on your plugs individually and make sure that they are all still good before you create a giant problem.