I don't think it's the light cycle. I think you may be using too much light. I've only really had luck with dim light cloning. I use a single 13W flouro for a 50 cell standard rapid rooter tray. I use 20/4 lighting too. But I've also used 24 hour lighting with success.
To much light, raise your lights they need to concentrate on root making not photosythesis and vegging.