Going back to basic and bypassing as much as possible, I connected the same guitar cable I used (to do the Return and Aux In tests at the back of the KPA using my guitar) from the Headphone Output jack of my FocusRite and going into the Aux input on the KPA. So its one guitar cable from my FocusRite into the Kemper, that's it, very simple. I actually tried 3 guitar cables with the same results every time.
I used my iphone to record what was coming out of my headphones (ATH-M50X) and attached it here
In the .zip file there are 2 files :
You Shook Me - Headphones from KPA.m4a --- The setup explained above, headphones connected to the KPA
You Shook Me - Headphones from FocusRite.m4a --- Headphones connected to the FocusRite.
We can clearly hear that one guitar is missing (or barely audible) from the "Headphones from KPA" mix.
Hopefully, this will get resolved soon! Thanks for you help, I really appreciate i!
Hugo