I'd guess you're not getting sufficient filtration. Try splitting your pump time into a morning and evening session and increasing the total time by a couple of hours (maybe 6 AM to 10 AM and 6 PM to 10 PM). If you're not brushing regularly that will help too; brush while the pump is running so that whatever gets stirred up can get filtered out.
You should probably also be running the pump when people are swimming (if you're not already). This will help get rid of the nasties the swimmers introduce and take advantage of them stirring things up.
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