It sounds like wolf tones from having the pickups too high. I noticed you said it happens with other guitars too though. So unless you habitually set all your pickups very high it's unlikely to be the cause. It should be a very easy exercise to check though. First measure the height of your pickups under both the high and low E strings (so that you can return to the current setup later if you choose). Now lower all pickups significantly. You need to do all pickups even if you are only listening to one of them as the problem is caused by the magnetic pull which still affects the strings when the pickup is bypassed at the selector switch.
If the noise disappears you have found the culprit and can start raising the pickups gradually until you get a sound you like without any interference. If it doesn't help just put the pickups back to where they were and at least you have ruled out another possible cause.
Yeah I considered the guitar as the problem at first but if I plug in my guitar to a real amp or the DI of preamp, its totally clean.
Another thought - I used to get "ghosting" when I used my Focusrite into Ableton and it sounded similar.
Do you get this same issue through headphones? Check that if you haven't...
Hope you find it soon!
It took me a second to test because the Kemper had been clean for a couple days but now the issue is back. I listened to the headphone output and its perfectly clean.