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How deep is your sand/gravel? It is definitely possible during siphoning you are releasing deposits of many types into the tank. At times I disturb the perimeter of the tank while cleaning the glass on purpose to release some "coral food" into the water, but try not to bother the substrate too much.
Have you tested the water that you are using during water changes? Are you using any type of PO4 absorber?
How many times have you siphoned it now? If it has been a good amount, a large portion of the "toxins" in the sand should be removed. Each time you disturb it (on a routinely basis), the less junk is released.
I've siphoned 3 weekends in a row. It looks a whole lot better, so now I'm going to concentrate on just removing water and leaving the substrate be for now.

