That just doesn't sound right to me, that the controller could have any influence in the way the sounds are produced, other than issues with touch sensitivity or after touch. There may be, and almost certainly are, velocity curves than can be set on the controller. That could have an effect, but other than that, the controller merely sends a message to the module to make the sound. No way it can change it or color it that I can see.
Hope to get my module back from Roland soon.
I'm thinking that the Roland guy has no experience with modules and controllers.
Don't give up yet Deane.
DonM