Are you sure that audio card setup is not doing the phantom routing?
For example, the default RME setup matrix routes all inputs to the 1 and 2 outputs, in addition to the normal in to out routing. I had to make the mapping only each in to its own output to make it usable by Cubase and the Control Room.
Everything is vying to be the go-to place for controlling your setup, but you have to work out which is in charge.