Oh goodness. This was almost certainly your problem then. The old used dry rock would have had a lot of dead algae and other things on it, which would start to decompose and create ammonia, which would then quickly overwhelm the low level of bacteria that you had in your lightly stocked tank.
At this point I think the answer is to ride it out with water changes and prime or amquil and bottled bacteria like we talked about, but I feel pretty good that this is the root cause.