I have resolved the Vintage Organs issue, sort of. I found that only one of my custom NKI's seemed to be affected. Resaving it from 5.6 did not help, there was no key switch rendering. So I recreated it from the original factory patch and that works.
It was my "clean" B3 patch with all the rotor disabled, no drive and DI selected for cabinate. This is my most used one as I will put it through Melda MVintageRotary or LX122. I suspect it was created before some up date to either Kontakt of Vintage Organs.