After much experimenting, it turns out that I was making it harder that it has to be. Mostly it seems to go away if you reboot. Sometimes you have to reboot a couple of times. Once greyhole picks up a file from the directory the first time it seems to continue to service it.
So, I have just been checking after adding each share. I have added all of the shares I need to move my existing stuff to the new system so I think it is stable for now.
Perhaps if I were not moving a bunch of big files to the server and watching it real closely I would have never noticed, if the problem "goes away" after the next reboot and if the fsck process eventually picks up the missed files, maybe it just is not noticeable most of the time. I don't know.
I am happy for the moment and moving about 1.5 TB of data to the new system. This will take a while.
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