I tried to find the correct compensation elements for a high voltage supply based on the application note https://www.analog.com/media/en/technical-documentation/application-notes/an118fb.pdf The schematic is here:
[![enter image description here][1]][1]


  [1]: https://i.sstatic.net/1CQtE.png

I used Bode100 to inject a test signal via a transformer across a 10R resistor placed between points A and B. I did a lot of experimenting and calculations with different compensation component values (both type II and type III). I measured the loop gain (B to A), the compensator gain (B to C) and the plant gain (C to A). The measured compensator gain always corresponded well to simulation results. Also, the plant and compensator gains added up nicely to give the loop gain. 

However, when I changed the R1 to a different value (10k) and R3 too in order to keep the same division ratio, the plant gain changed with all other components left unchanged. Why? I think the plant is independent of the compensator here. The only thing I can see changed for the plant is the loading of U2 but this should be insignificant, especially at low frequencies (10Hz) where I was the plant gain change.

Any ideas why the measured plant gain changes?