Do you have a Turkey Baster??, if so, blow the rocks off and syphon off any debris. Give the tank a day and then see how it is doing. You have been cycling for a long time now, probably got the cycle completed.
I am thinking that there may just be a little debris over the rocks that is dye off, if so once the rocks are blown and a water change is done, syphoning off the debris, you should have perfect levels.