In these instances are you adding to the gain knob's "default" setting, Chip?
When a Profile is made, the KPA's software determines the amount of gain it perceives was set on the amp. Raising it beyond this point forces the unit to guess what it might've sounded like if the amp had been cranked more, resulting in what I've always called a "synthetic" sort of "spongey", lower-attack-definition sound.
In practice, lowering gain from the default setting generally sounds great. This makes sense 'cause the Profiling routine passes audio at "all" levels through the amp and analyses the result but there's no way to know how the amp might've sounded should the gain knob have been set higher.
I dial out the presence, high EQ register and play with the amp bias, shaping and ect.. It's still there
Have you tried starting with lowering Definition before adjusting any of those things, Chip?
Also, I'd avoid raising "Clarity" if you find the top end at all harsh.