There are no moving parts in the filter compartment. Make sure the rubber ducky is not screaming for assistance. The 2 filters also don't move so you can eliminate the fact that they might be rubbing against each other.
Are you sure the noise is coming from the filter compartment? It almost seems that something may be stuck in the impeller of the circ. pump. You won't hear it when the pumps are on high, it drowns out the noise.