Phosphate leeching from the rock into the base of the coral.
It could be flow, but from your description, I kinda doubt it. I feel the same on lighting issues, but only if the specimen is overshadowed or has overhangs shading it.
How old is the rock it's on, and is all the rock in your system the same age??? Is this the only specimen doing this on that piece of rock?
The phosphate leaching occurs as the rock's internal circulation of pore water becomes saturated with phosphate as a result of accumuation in a tank with many fishes. Even in systems without flake feeding, this occurs as export cannot keep up with the feeding inputs for the fishes. This is especially true if lots of macroalgae is used to feed the fish and skimming is inadequte. The phosphate will not show up in hobbyist's test kits as the phosphate is bound to the rock when the phosphate in interstitial waters adsorb to the pores of the rock. This will be especially true if you have good circulation in the tank, or if you have reused rock from tanks with a long history of fish in the same system (or poor water change husbandry)...
Just a wild guess.
If the rock is on the substrate, phosphate accumulation wicking is more likely to be the issue, as the sand contributes to the wicking process of phosphate salts and creates a microenvironment where detritus collects in eddies at the rock base. Its decomposition creates nascent free phosphate for adsorption to the CaCO3 of the rock, then as it accumulates in the pores, the production of phosphatASE enzymes by the rock's bacteria gradually release the phosphate from its adsorption sites in the rock pores so it then can be wicked through the phosphate-saturated pore water circulation. Specimens directly adhered to the rock will then aBsorb this pore water through the skeleton (wicking) and the high levels of phosphate then begin to shut down calcification and coral tissue growth from the base up. This is not to say that you don't have some benthic coral parasite that emerges from hiding at night and eats from the base up (unlikely unless you're seeing this condition in multiple specimens in that location), but from your descriptions of the conditions, etc, the phosphate wicking is a likely scenario in a closed system like yours.
HTH