I have read about a crash in the cycle causing this. If you have too much water circulating through the reactor, the bacteria strip the tank clean, then have nothing to feed on, and die off. Then the nitrates come back and the cycle starts over. This is why the reactors that allow you to limit the water flow through the tank are becoming more popular. They allow you to have enough water movement in the reactor to keep the pellets moving but still limit the water going in and out of the reactor. This is why I am using a Ca reactor for my biopellet reactor.
This is a common problem in closed systems with limited resources. I learned about this in collage ecology. We read about moose on an island that ate most the available food. The moose would then die off and the food would grow back. Once the food grew back so did the moose. This cycle will just keep going unless there is some sort of intervention. With deer in the country we grow crops so there is no food limiter and their population has grown out of control. In KY we no longer have a limit to the number of doe you can kill.