I've seen the same issue of external cloning that is sorted with KKS removal, however it goes further.
Once I remove KKS no clone remains outside the pod after boarding but I do get a clone inside the pod when I transfer Krew internally. My Kerbals are all there and appear in their portrait windows with an extra window showing static and the name of the said clone. Access to the cutaway view is disabled as well. Reset to normal is possible with a trip to the space center and back to the craft involved.
It's obviously not KKS and I'm working on narrowing down the combination of mods that causes this. Only 96 to go!! I'll update once I know.