Thanks for replying Chewy. It was awfully quiet on this post.
I have tried repairing all permissions in disk utility, and directly in terminal. I tried making a whole new user account on the system drive, so there are no preferences at all until Nuendo builds them for the first time, and it still has this problem. Interestingly, another user account that I made earlier this year does not have this problem, even though I am also launching Nuendo on it for the first time. So it is probably not disk permissions. And all these User accounts have identical administrative permissions.
Seems like it is related to Media Bay and scanning, but unselecting and reselecting drives and rescanning does not solve the problem. Also occurs in N5… so what does that tell us? This one is a brain twister for me, but it is a really big problem with my work schedule!