STN/RTN:
Possibly due to rapid changes in lighting spectrum/intensity with new DIY LED system, yes ? Also, the red spectrum is one that is not experienced by "most" reef building corals in the wild, as it is filtered out within the first few meters. In artificial situations it can/will cause STN/RTN ! Likely "one" of the causes of your photography enigma(s) as well ... I strongly suggest lowering these drastically, if not eliminating them.
NO3:
What is your filtration philosophy/implementation, especially in regards to NO3/PO4 ?