Franco,
Can you please post a model showing how the RT Box based controller is implemented? If you would not like to share your model publicly, then please reach out to support@plexim.com.
I’m also interpreting your situation as a) offline simulations in PLECS show the expected response b) behavior is correct for external MCU based controller connected to the RT Box and c) when modeling both the controller and plant in the RT Box, the result is distorted. Is that accurate?
Thanks,
Bryan