I had surgery back in November and neglected the pool for a couple of months. Definitely had super high pH for a while (was purple a few times) and had terrible wind storms with a ton of debris that sat in the pool for weeks. By the time I cleaned it up that's when I noticed the stains under the debris.Unsure. Did you have high CH and/or high pH in the past that might have created the scale? Scale can form with dirt or other organics in it and look like a stain. But the puck should have lightened it as it is acidic and would cut through the scale.
Original theory was that it was organic... maybe some kind of sap or something, but shouldn't the slam have taken care of that?