Thanks guys. I've been doing some more playing and testing today while switching between my amp and the Kemper. I'm starting to get the feeling that while I can get the tone of the Kemper very close to that of my amp at a specific volume, the built in amplifier just doesn't respond like a guitar amp at all, it's more HiFi or PA like.
One test I've just done is start with a medium drive sound which at average room levels is very hard to differentiate between the two systems. Then if I put the guitar on a stand and slowly increase the master volume of each amp while just rubbing the strings it becomes very apparent that they react in a totally different way. With the amp as the volume increases the strings become more and more sensitive to touch, with the KPA they don't, things get louder but the strings almost become more buried in the noise.
As you say Raoul, I'm starting to think thing that moving to the KPA requires a different train of thought, it's more about comparing what the front of house sound is like through the PA with the KPA vs an amp with a mic than what the guitarist experiences from his amp. This is maybe why rehearsals are sounding a little rough as the PA system is behind the drummer and not the best PA in the world. This mixed with the less defined sound coming from my cab is probably not ideal.
I think I'll try running the KPA in to my amps power stage and see what effect that has next.