When using KatanaMan with your Katana amp, it is important that you do NOT have the amp "Tone Setting" set to 'Panel'.
If you do have the amp set to 'Panel', each time you turn an effect (eg Boost/Mod, Delay/FX, or Reverb) OFF then ON, by using the foot switch or KatanaMan's bypass button for example, the amp will reset to the value currently set on the amp knobs, not the patch setting. This is likely to cause significant audible anomalies to arise.
For example, if your amp Boost/Mod knob is set to 0, and your patch is using a boost device with high gain/level, if you turn Boost/Mod OFF then ON - using the foot switch, bypass etc - the amp will set it's (and the KatanaMan) Boost/Mod level to 0 rather than whatever Boost/Mod level you had set in your patch.