It sounds like you are over feeding to me. I can testify that BTAs do not mind "dirty" water, however IME swings in water they do not appreciate. You might want to google silversides and nems as well, I have read that they can "spoil" and subsequently kill your nems. After reading that I stopped feeding silversides all together. As long as you have good lighting your nems should be fine being target fed brine shrimp. I also like to give mine spectrum pellets (the 1mm ones)