1st item, don't worry about differences in the settings on the volume knob. Those settings or "%s" as you called them are completely arbitrary.
Next item, don't worry about changing speaker positioning with a new amp. The amp has nothing to do with the positioning of the speakers and the room acoustics.
Since it sounds great/similar to the NAD for other connections, it makes me suspect that you have something going on with the CD input, perhaps some setting but I would think pure direct would eliminate that.
Did you try the RCAs on one of the other inputs, like 1 or 2?
What CD player?