If the brown stain won't brush away...

[docsobeck]

thanks janet, but that's not the one i was thinking of. that was a spring stain, this one is recurring. i guess i imagined it.

so let's say that it is organic. why/how would it be impossible to brush/scrape up, and why/how would it keep reappearing in the same spot? that's the part i can't wrap my mind around.

and if it's not organic, why/how would it respond to higher levels of FC?

BTW, i have 0 CC, and when i shock the stain goes away but then comes back when the FC gets back to lower levels.

[waterbear]

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.

[docsobeck]

i agree that it must be an algae issue, but i swear there is no roughness, pits, divots, or anything at all different about the places the stain appears. very strange.

it's a light brown color, not yellowish at all, but not dark and really noticeable. it's easier to see when the sun is bright; when it goes behind a cloud, it's very difficult to see. guess i'll just have to be more vigilant about keeping my FC level up.