So enough about system stability.
I REALLY think you have a testing issue, unless SOMEHOW all that SW is going into your ATO and being replaced with RO/RODI
Have you considered taking a closed container water sample to a LFS for Sg testing?
One of our members here recently was having Sg issues and it turned out his refractometer was damaged. He would calibrate it and then it would slowly change by itself. He bought a new one and problem solved.
Doesn't explain your controller issue, but it's possible it's also having issues.