Dosing any form of carbon has its drawbacks on the bacteria. Your giving a new food source, one that may be rather limited in our systems. Carbon.
In a system that has nothing dosed, doesn't run any extra equipment and no other doodads the heterotrophic bacteria break down organics into ammonia. the autotrophic bacteria then take that ammonia and thru a few processes turn it in to nitrate and in healthy conditions into nitrogen gas.
when you carbon dose your giving the bacteria a new, formerly limited, food source. the ratios between N & C change and the heterotrophic then take advantage of the extra carbon and become the main nitrifiers in the system. they are able to convert ammonia straight to nitrogen gas and bind nitrogen to their beings, no nitrites or nitrates are put into the water column. this may starve the autotrophic bacteria of food since the heterotrophic bacteria are able to propagate several times faster then autotrophic bacteria. BTW bacterial blooms (of the common cloudy water type)are often heterotrophic in nature. The side effects of having heterotrophic bacteria as the main nitrifiers is bacterial flock, and lots of it. autotrophic bacteria's side effects are nitrates, heterotrophic bacteria's is excess bacterial flock.
With the autotrophic bacteria's numbers limited they are either getting their food source from any excess nutrients in the water column or from the rocks. the water column would be a first priority because its easier. pulling nutrients from the rocks takes more energy and bacteria are lazy. With the impaired autotrophic bacteria population impaired they wont be able to keep up with liberating phosphates from the rock, thus leading to excess nutrients within the rock. this could be why some of your corals RTN and some don't. some rocks may be full of nutrients and some are not. You can test this by taking one of your corals that appear to be doing good and switching it with one that's not so well off.
Detritus. Like I said before, heterotrophic create a lot more bacterial flock when you carbon dose. if your not exporting more then whats being imported (IE: Siphoning your sandbed) that bacterial flock is going to settle in your rocks, sandbed, nooks and crannies of your rock and further decompose releasing inorganic N & P back into the water column, the same N & P you just bound to the bacteria flock by carbon dosing therefore making carbon dosing a problem, not a nutrient exporter. OP stated when he took the phos reactor offline phos went from .03 to .09, wonder why.
http://m.avto.aslo.info/lo/toc/vol_43/issue_1/0088.pdf
https://marine.rutgers.edu/pubs/private/AmmermanEEM02.pdf
http://www.sciencedirect.com/science/article/pii/S004484860600216X
http://www.ncbi.nlm.nih.gov/pubmed/24186453
http://www.scribd.com/doc/182676082/Understanding-Heterotrophic-Systems
You can believe what myself & Reefin' Dude are telling you, you can read for yourself, or you can continue what your doing and wonder why your system is failing. I dare you to try it our way.
