Hi Hoogie,
I think I can help you. First, the staining you see is a symptom of a much more expensive problem - corrosion of your copper heat exchanger. Metal corrosion is caused by acidic water, or water that has too low pH, therefore too much acid. Remember that in a fiberglass pool, the pool surface does not alter the water chemistry at all. If you are using tablet form chlorine (3" or 1" tablet) this is likely the cause. These little tablets are really convenient, but very, very acidic. Tablet chlorine has a pH of 2.9 - a lemon for comparative only has a pH of 2.0!! So, as they dissolve, they drop acid into the water. In a fiberglass pool, the surface isn't dissolving alkalinity into the water (as plaster does) so there is nothing to counterbalance this effect.

First to prevent the problem, watch your pH carefully and adjust weekly to 7.6. This will protect your very expensive heat exchanger also. Your test kit will tell you that 7.2 is "normal" however, we are "reading colors" which is a subjective matter. Keeping your pH a tish on the high side is less destructive than on the low side of normal, and you have a cushion, just in case you go away and forget to check it. Low pH is very destructive!

Now, how to fix this problem?? Easy. You can, of course use muriatic acid on a fiberglass pool, provided it is a quality shell. If it is an Aloha Fiberglass Pool, there is no problem whatsoever. I can't speak for other manufacturers. Be careful, though, Muriatic acid is nasty stuff. Wear your protective gear if you use it. But, there is another product that is nealy 100% effective at removing the stains, then keeping them away- Metal Magic by Haviland. 800-333-0400. Unlike Jack's Magic, which works some of the time, but not all of the time, because it is a sequestrant, not a remover. The first time you suprchlorinate, you destroy the protection. We've had amazing success with Metal Magic.

To keep the stains away, keep that pH at 7.6 check weekly and adjust as needed. Keep a metal removing agent in the water at all times. Metal Magic is a good product for that.