Hi Uddhav,
The update rate of the analog output update rate is equal to the simulation time step (the "large one", used by the SPC, which is probably around 300-500ns). It is not as fast as the UltraCore step of 4.5ns on HIL101. This is a fundamental limitation in the hardware. In your case it looks as if the analog outputs are updated every 500ns. If you reduce your time step, you will have a better update rate, but best case scenario is 200--250ns, which will not yield fully smooth waveforms at 100kHz.
Is your controller directly sensing the transformer current in order to derive the control?
Best,
Jovan