Thank you very much for your report, I just managed to reproduce this problem in Cubase, as you described it.
Some parameters in Vienna MIR Pro are being smoothed to avoid clicks, e.g. when you switch on an EQ or switch off the direct signal. This parameter smoothing is only performed while audio is running.
As soon as I was playing audio for a few seconds before recording the output signal, the output signal is fine. Loading a project and recording the output signal immediately works also fine, the only critical case is the one you've described: changing parameters after loading a project while audio is not running and then recording it immediately.
I'm afraid this problem occurs 'by design' and is not a bug that can be fixed. I'll look into it to confirm this, and I'll check why the parameter smoothing is not completed after one second - normally after 100ms all parameters should be completely up to date.
Best regards, Florian