How big is your pump? A lot of times people have pumps that are too powerful and they simply force stuff through the filter media right back into the pool. Can you actually see the stuff coming out of the return jet or does it just reappear on the bottom of the pool? By the way, there is no reason to change sand. It does not wear out. Sometimes you have to top it off a little but not replace it. I have had the same sand for 12 seasons.
OR --- It might just be dust and dirt. My liner pools have always had the same situation. I can vacuum and get the floor clean but that is only because the dust is suspended in the water from movement. Then, it settles right back down into the lines on the floor caused by the liner seams and also where the pad underneath the liner is taped together. No matter how clean I think the pool is, those "lines" always reappear. I don't think there is much you can do about them. There is no possible way to get rid of every single speck of dirt/dust in a pool. Once people are in and the water is moving, it all goes back into suspension so you can no longer see it. No big deal.
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