Rocks in the sump can be good and bad. You need to make sure you rinse them every once in a while or have some CUC members down there or they can collect detritus and actually become a nitrate factory. I had this issue, it was making me crazy and then Spanko pointed it out to me, a simple thing that is overlooked a lot.
If the rock is DRY base rock, it can go right into the sump.