It is probably a combination of a few things. #1 is everything that was alive on the rock died, and if you didn't at least soak the rocks in water or powerwash them to remove the dead organic matter, this stuff just goes right into your water when you put it in the tank.
#2 is bound organics and this would be the result of whoever had the rocks prior to you, and their husbandry practices.
You can get rid of #1 by doing a large water change and if you didn't wash the rocks at all, I would do this (the water change, not washing the rocks) just to make things move along quicker. I wouldn't rule out a 100% change really. Just get the fish out and acclimate them to the fresh SW over a few hours and they'll be fine.
But then #2 will take some time, between scrubber and GFO (I prefer Phos-blast from Premium Aquatics, which is RowaPHOS just cheaper) you should be able to get everything under control.
Or, you can just let the scrubber do it's job. With very little bioload and feeding, it should do what rleahaines said - it will mop up N fast, and P will probably still be there - so you're then back to a PWC or GFO/Phos, once your P hits zero pull the Phos remover and monitor