Hi
I have found the problem with using the small and PCB mount transformers is that they run hot due to their construction.
The manufacturers do not expect great efficiency, and to keep lamination noise to a minimum they weld the laminations together down two sides.
This changes the magnetic characteristics as well as causing eddy currents, this will distort the output waveform as the magnetic field is just about saturated in the core. The flat topping of the voltage waveform could be field saturation.
If you have available to check if this is the problem, try a larger transformer that hasn't got its laminations welded together.
Also is the CT inline so it is not measuring the voltage sense transformer current?
The thread is getting so long its hard to follow, so if its already been mentioned, then I stand corrected.
Tom...... 