Ok, tried that last night..... preamp output connected directly to the console, compared guitar plugged directly into preamp, to guitar plugged into kemper, kemper direct send to preamp input. They sounded exactly the same but that is what you would expect considering the direct send from the kemper is just a pass through of the guitar signal. The difference I was hearing before was from the kemper main outs during the profiling process. What viabcroce posted might be an explaination of what I was hearing before but it did sound like an EQ boost - a sort of pre-emphasis.
I spent a few hours profiling a different preamp last night (Triaxis). Taking into consideration what others have said about leaving the cab section on, I created a clean non distorted profile. The results are what you would expect... the profile sounded identical to the original. It was very interesting that after finishing the profile, switching to browse mode and listening to the profile, switching the cab on and off made no difference in the sound....... ok, I'm getting it. Now I'm going to do a little more experimenting with regards to which Triaxis preamp output to use when profiling, the cab sim or direct non-cab output.
Thanks to everyone who posted for the advise and tips.
Try with the preamp connected directly to the console, but go through the Kemper on the way in (Kemper in profile mode). Does it sound different? Use the same cable from guitar>Kemper as you use from guitar>preamp when comparing.