Have always wondered why people put live rock rubble in the back chamber of an all in one tank. IMO too little of an amount to really make a difference, and if you are going to do that you might as well leave the bio balls in and do a cleaning schedule on them. So yeah, you probably have a goodly amount of detritus sitting on the floor back there contributing to the nitrates. How often are you replacing the chemical filters? I usually do it around the 5-6 month mark and also replace and light bulbs at that point too. Kind of like turning the clocks back and changing the batteries in the smoke detectors, one thing triggers the other.