I am having the same staining problem in Florida. We built the pool 5+ years ago and it had a salt chlorinator. Never had any stain problems. The salt cell broke and I haven't replaced it yet, so I've been shocking the pool. The brown stains started showing up a few weeks ago. I first thought it was dirt on the bottom of the pool. But it didn't come off when I brushed it! I found a term online - dirt scale. Is anyone familiar with it? Pool stores in my area don't know what I'm talking about. I put Jack's magic Metal Plus in the pool today, went to Home Depot and bought pvc piping, poured murianic acid down the pipe over one of the stains. After scrubbing it did seem lighter. This will take several hours if done this way. Any other suggestions?