I know thats the part I didn't understand but if you look at the two sets of pics its not just the orientation of the stains. They are next to the exact same liner patterns. Those spots havent moved an inch.
Does the pool water get close to 60 degrees in the winter? That's about your average high temp in Jan and Feb right? Seems possible you could get slow growth during those months especially near the water line if your FC is 0.