I think Burkhard is right that to get to the root of this, simplifying the process for now might help find where the problem is.
It would only mean muting one mic just to test.
How far out is the created Profile from the source? Slightly out or a night and day difference?
If it’s slight, you can most of the time salvage during Refine. When the Kemper overshoots the gain, bottom and and mids, I normally do some discordant harmonics to get back on track during Refine after adjusting the gain on the Profile to match the source (if the gain has overshot)
For instance…. During Refine, playing harmonics across all strings..…
4th fret bottom E, 5th fret on the A string
4th fret A and 5th fret D
4th fret D and 5th fret G…..
Same pattern up all the strings.
Another harmonic pattern I use is…..
3rd fret bottom E, 4th Fret A and 5th fret D
3rd fret A, 4th fret D and 5th fret G
All the way up the strings.
I did have a situation where the Profile was completely out and I couldn’t fix it. That was on one of my 70s 50w non master Marshall heads.
Had the volume on 10 and the resulting profiles were completely freaked out. All muffled bottom end and distorted. Knocked the volume back to 8 on the Marshall and it would the profile fine.