The stains appear to be organic, but sometimes a pic doesn't do us justice. You might want to post a full set of test results to go along with this as others will probably want to know as well. You mention "after all is clear", so I'm assuming you recently cleared an algae situation? If so, that would tend to indicate residual organic staining at the bottom that may require a slightly elevated FC level for a couple days or so to help resolve. As a test, you could always try rubbing a chlorine tab on one area, making sure to not let the tab sit in one spot too long, but enough to see if the stain reacts to the chlorine tab. If it does, it's organic which would require the elevated FC level to help remove it - along with daily brushing.