This may be obvious to most, but I thought I'd post it anyway.
I have a Gr-55 that I return in stereo to the loop of my the KPA. X Slot and Stereo Loop.
My Godin guitar connects to the GR-55 via the 13 pin cable, so anytime I'm playing Gr-55 synth or modeling sounds, the sound is coming in through the loop of the KPA and not the regular input. This means that the Input light of the KPA does not light up at all.
Tonight I noticed that the Master light was hitting the red. A light bulb came on, and it dawned on me that the master section of the KPA can be overloaded just by returning a hot signal though the KPA FX Loop.
This might explain some of the confusion people are having with Master light overloading, while the Input light is not. In my scenario, I was able to overload the Master section with just a hot signal returning in the KPA loop. Adjusting the input sensitivities would have had no effect on the Master section clipping.
The only way to stop the Master section from clipping in this case would be to go into the KPA loop and bring down the volume, or turn down the volume of the effect returning into the loop (in my case, the GR-55).
I know sometimes, I've been confused as to why my KPA was overloading the master section on some profiles, and not on the others. Now I have another thing to check.