Sounds like white water mold to me.
Hum, take a sample of the "flakes" and water if possible to local pool store for analyzing.
If you have a Salt Water Chlorinating system and hard water to start with, then what you are seeing is calcium precipitation. Water can only hold a certain amount of dissolved minerals. When sodium is introduced to the water, it displaces the calcium which precipitates in an insoluble form and builds up inside the ion exchanger. The flakes break loose and are introduced to the pool via the water return lines.
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