I FEEL YOUR PAIN! I have been running in circles with metal stains all summer. I first noticed them after I opened the pool and have been battling them ever since. I have had tap and pool water tested, no metals. I have drained my pool 3 TIMES! No luck. I have replaced all potential rusty screws. No luck. I have used every kind of sequestrant, no luck. The stains reappear if I raise my FC over 2. It has absolutely drove me nuts. So...I basically deal with them unless we have a party or company and do a quick AA treatment right before so it looks good for a few days. The only place I can think of that the metal is coming from is runoff from our deck into the pool, but I am not even sure that's the case.
By the way, there was one time I used a cheaper sequestrant and woke up to a cloudy pool the next day, which had never happened before. After two days of frustration I added a bit of clarifier and it was totally clear in 6-7 hours, but it did cause my psi to rise a bit so I back washed.
I will follow your thread and hopefully you will find a magic cure! Good luck to you!