Your guitar needs a proper setup. If there was a problem with the kemper it would sound bad no matter where you play on the neck.
All 3 of my guitars sound like this and have the exact same issues.I treat them like my babies they are well looked after and dont need setting up and they are awesome through my Rockerverb MKII i dont have this problem at all and the clean tones on the kemper sound amazing with no issue again its just the distortion.Im thinking maybe its the interface or it could even be the DAW (Cubase 5...yeah its old but Hey DAWs are very expensive) im gonna run a test and record some guitar in a different DAW see if there are any changes.