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When you're in Program mode, the Mute buttons always control KB3 effects. In a setup
containing a KB3 program, if you want the Mute buttons to control KB3 effects, you'll have to
edit the setup, because in Setup mode, the Mute buttons mute and unmute zones by default.
1. Go to Setup mode, and select the setup you want to edit. Press Edit.
2. Press either more soft button until you see the COMMON soft button. Press it.:
3. Select the Mutes parameter and change its value to KB3 Control.
4. Don't forget to save
I would check that first before moving on to possible hardware causes.