Hope this makes sense. I've recorded a Hammond organ part using Acid Pro 7 and the VB3 plug-in. When I play back the part I've recorded I can use the modulation wheel on my controller to change the speed of the Leslie sim. Is there a way to record these modulation envelope changes as I'm playing back?
From what you've written it would appear that your existing "recording" is of the MIDI data, i.e. it is not an "audio" track, and given that I haven't tried this myself, since those mod wheel changes are actually all MIDI control messages, have you tried "recording" those messages to a new track, ensuring that the output of that track is set to the same MIDI channel as your VB3?