I have an inground pool with an Aquarite SWG, but I believe they are probably all similar. Sounds like you are not running your pump nearly enough. I run my pump for 9 hours a day, and have my SWG set to 40%. Every pool will be different however.

As far as the flakes, that would be a bi-product, I believe calcium chloride. You may need to clean it with some muriatic acid and there should be directions in your manual.