Your problem may be that you do not have enough disolved oxygen in the tank for your biomass... you did not describe the filtration, but different species of rays have different oxygen requirements. I have seen tiger rays die slowly in a tank with black rays and motoros that were not affected due to inadequate aeration. There is NO sign except death.....except, sometimes the rays affected by low oxygen may be quieter than the others. You should add a power head or be sure that there is adequate water turnover especially if you do not use a wet-dry type of filtration system. I do not think it is the substrate, the nitrates, water changes, or pH..those parameters sound OK. The only other thing to consider is an air intake leak in your pump that may be causing air embolisms in the fish. If your pump is powerful enough and there is a leak in the intake side [not the outflow] it will suck in air and then pressurize the air which becomes disolved in the water, is picked up by the blood as it pases through the gills, and then deposits in various organs in the fish....depending on where the air bubbles are deposited, it can be fatal [in the brain, for example] and there are no outward signs. As in inadequate aeration, some species are more sensitive to air emboli than others....good luck.