Hi,
Some might call this a feature while others call it a problem. Either way it's on purpose.
When you plug in stereo inputs the pedal automatically goes into true stereo operation regardless of how many outputs are plugged in. That's why you hear a volume difference.
If you still want to use it in this configuration you could compensate for the volume difference by saving your preset with a lower output volume. (This feature is new in V3 software.)
-Alan
