Are you using anything stronger than vinegar? Strong acids will do this. If I want something really clean I first soak it in straight 5% white vinegar and then put it in the dishwasher. Of course you cant do that with the motor but the screen may just have some build up and provided it doesn't get on the heater in the dishwasher this will clean it up like new with no harm.
I'll try that but I know it's not coraline since the tank's only a week old and I haven't even started adding calcium to the water yet. Should I do half water/half vinegar.
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