Re: If the brown stain won't brush away...
There is fungus from the soil that can grow UNDER your liner. Not much that can be done about it until you change the liner. Chlorine and fungicides are the usual treatment of the soil at liner change time. Some people have reported success by applying a fungicide (often copper based) to the soil around the liner and soaking it into the ground but YMMV.
What color are the stains? The ones from under the liner usually look blackish.
Also, this type of fungus is not really affected by chlorine levels in the pool.
If yours only appears when the FC drops it sounds like common algae, especially if it is brownish. As to why it appears in the same spots, there is a good probability that they are rougher than the rest of the liner (perhaps from the brushing to try and removed the stains). Algae usually appears first on rougher sections of a pool where it can attach itself.
Retired pool store and commercial pool maintenance guy.
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