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It could be ulsers? try treating for bacteria infection see if that works.:happyfish

Is it fish only tank? If so treat with coppersafe. If not use QT for treatment. Also you might want to invest in a UV sterilizer for your tank.

It sounds like brown jelly. If that is the case you need to remove the flower pot from the tank and treat as soon as possible. remove as much jelly as you can with a tooth brush and then do a cold soak for several min. to kill off any bacteria left. If you don't it will spread over the coral and...