That is strange, I just did a whole tear down on my 40g to replace the substrate, it was crystal clear in 6 hours using a Remora Pro skimmer and Penguin Biowheel. I agree, it does not sound like sand. I would go with an algea bloom. If the tank is pretty new it will need to ride it's course. While this is a mixed opinion, you may want to try some carbon in your HOB for a day to see if it helps. What kind of skimmer do you have, on my remora you can adjust the height of the collection cup, the lower it is the more wet the foam will be and the faster it fills, the higher it is the more dry it is and the slower it fills.
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