With live rock, the ammonia should have converted to nitrates quickly. I believe that if Live rock does not see ammonia for a period of time, the bacterial populations of the nitrogen cycle decline. The rock you have might have been fallow for some period of time. In your tank, it might be like starting from scratch. Even starting with sterile dry rock, salt water, ammonia and water movement, eventually the proper bacteria will colonize and proliferate. It just might take a few weeks. You can accelerate the process with bacterial cultures for this purpose from the LFS.