This is normal for the wiring scheme you selected. It's how the volume knobs work on a Les Paul type guitar. A Les Paul doesn't allow you to adjust the blend level between the two pickups. When the switch is in the center position, both volume knobs affect both pickups.
In order to fix this so that you have independent volume control, simply swap the lugs of the pickup wires with the selector switch wires on the volume pots. Basically, you want your pickups connected to the pot center lugs, and the selector switch wires (output jack in your case) connected to the left lugs. The ground connections stay the same.
Rickenbacker Club #506
Last edited by Projectile : 10-13-2013 at 09:16 PM.