So what do you think I should do? Put gfo on the tank? Take the pellets off?
Before you do anything you want to be sure that they are dinos in the tank. If they start to form snotty strings and/or you start getting bubbles in them then it is likley dinos and you could be in for a difficult fight. Hard to say what action you should take as conditions are going to be different from case to case.. Best I can do is detail for you my case and you can make a determination if there are any similarities.
There are many ways to address these, most use high PH, higher if possible and light deprivation cycles. You want to dose beneficial bacteria to help out compete for any food source the dinos might be scavaging. In my experience though the dinos can bounce right back so long as the pellet reactor is still running. They seem to feed either directly on pellet material emiited from the reactor or bacteria that is sloughed off the pellets and ejected out of the reactor.
In my tank I had only a few acro frags, and a high fish load. The reactor kept up with my heavy fish feeding and I could never measure any PO4 or NO3 leading up to and after the arrival of the dinos. Even during my initial lights off period when the dinos all died off I could not measure NO3 or PO4. Even though my skimmer was well up to the the task and load, I think my problem was due to a lack of bio-diversity (corals and other filter type feeders) combined with a heavily active pellet reactor... more a little later.
In my experience these reactors are very efficient at what they do but they do not "slime" up. At least not to the point where you see bacterial strands bouncing around inside and/or ejecting from the reactor. You may get a few at the bottom inlet, but mostly the bacteria clings to the pellets and you can't discern them with the naked eye. What you can see though is all the material ejected from the reactor if you either direct the effluent into a clear glass of water or actually remove some pellets and rinse them in a clear glass of RO/DI water.
My point is that there is alot of material ejected from these reactors when they are active. In the absence of any real biological competition for the ejected material, a scavanger like dinoflagellites that does well in low phosphate, low nitrate, high carbon enviroments seems to flourish.
I eventually removed my pellet reactor during my second attempt to weaken the dinos with a 7 day lights out period. This made a tangible difference, but they still grew back in a few areas, albeit much slower and in fewer numbers. I theorise that they are still feeding on whatever leftover material was ejected from the reactor before I removed it.
My last ditch effort before I tear down the tank and sterilize it is to use Ultra AlgaeX by Fauna Marine. Says right on the bottle it is formualted to combat dinoflagellates. This is a very aggressive treatment though and anyone should do thier homework before taking this route. It can stress/kill other sensative corals and fish if you are not careful with the dosage. All my acro frags were previoously killed by dinos, and all my fish have been moved to quarantine so I can afford to be a little aggressive with this stuff. I am on my fourth dose of AlgaeX without having to turn out the lights and I contiune to feed the tank... it is working, albeit slowly. I can't say if it wil ultimatly work or not just yet though.
Too sum it all up... I think where I went wrong with my tank was having too many fish and not enough corals in combination with the pellet reactor. If I were to do it differently today I would build up filter feeding bio diveristy while slowly ramping up the fish load.