Hmmm. That's strange. Can you tell if it is a particular type of substrate that you are using? If so, maybe you shouldn't use that type anymore. It's very strange that you didn't experience this problem when you first set up the tank especially if you are only now seeing this problem. I am not sure what the problem is or how to fix it. We'll see what other members can think of.
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Phishie
Site Coordinator

"An ounce of prevention is worth a pound of cure."