All the Kontakt guitars I have tried all play in the blue keys.
I haven't got into Kontakt programming but maybe you can go in the wrench and Mapping Editor or the Script and change things then save it as a new instrument ?
Maybe ask in the Kontakt forum.
You would think if you are sending the keys to those octaves you would get the correct sound ?
When you transpose it is the low E in the midi playing on the first blue E ?
Whats the Chord Mode Chord-keys on ? was that on when you tried transpose ?