There are multiple potential causes of the problem you're having. It may not be anything wrong with your system but an infection your coral had before you got it and the stress of moving may have just accelerated it's progression. One of the problems with determining the cause is a "healthy" looking coral may infact have a severe bacterial infection and it is just a matter of time for it to become obvious. As far as treating it the antibiotics I've seen in research papers used to treat bacterial infections are not readily available to most aquarists and treatment would have to be done in a hospital tank. I know locally one of the maintenance companies introduced a pathogen with some wild collected corals and had to find a vet who gave them a perscription, then had to move the corals in question to a hospital tank to treat them for a coupel weeks before returning to the system.
Treatments, in addition to dipping, you might try that I've had some success with are siphoning off any dead or diseased tissue first to minimize spreading any infection then:
fragging it above the line where the probelm is obvious and superglueing the edge.
Just superglueing it has worked in some situations.
Using lugal's iodine in a syringe and with the nozzle just a couple millimeters from the tissue and bath the areas in question with iodine (make sure not to exceed the recommended iodine dosage for your aquarium)
Use H2O2 instead of iodine.
