Hi Stone;

1. Put some scale in a glass with white vinegar. Cover it with Saran wrap and leave it overnight. If it bubbles or dissolves, it probably carbonate based and can be cleaned up with various acidic products. If it doesn't do either, it may have to be removed mechanically.

2. Put a Vitamin C tablet on a stained area. If the area is lightened when the tablet dissolves . . . it's a metal based stain. Otherwise, it's not, or at least, probably not either copper or iron. Organic stains can be left from "yucky water", and are frequently removed by high chlorine + time.

3. Quote: "the water chemistry has been maintained properly". Our ideas -- BBB method ideas -- about what "properly maintained water" is, and standard pool industry ideas about it vary from each other quite a bit. Get a K2006 (link to Amazon, or you can search Google). Be SURE to get an FAS-DPD chlorine test; the K2005 is NOT the same!

Let us know what you find.