j_beau..... here's what I think.
I think your refractometer needs calibrating with 53ms calibration fluid. (not ro/di)
From the looks of your numbers with RC, it looks like your refract is off about .002. Meaning, you tank may not be at 1.025, probably 1.023
That would explain the low calcium and mag levels of RC.
Contrary to popular belief, many refracts cannot be calibrated with ro/di.
I would buy some Pinpoint 53ms calibration fluid and calibrate the refract with it. Then see where you s.g. is.
Mind you, none of this has to do with the original problem posted of low pH, but I think your cal and mag could be a little higher.