with CYA of 30, you should not be letting your FC drop below 3ppm, ever. To find out if the stain are organic, you can try holding a trichlor tab in the area for a few minutes, if it lightens, you have your answer. If you suspect it is metals, rub the area with a vit C tablet and see if it improves. Lastly you should perform an overnight FC loss test to see if you need to shock. What is your CC level?