So there is a workaround fortunately! Calibre has the capability to have the metadata database in a different directory from the library itself. You need to set it with the full path including the name of the database file in an environment variable named:
This is documented here: http://manual.calibre-ebook.com/customize.html
This link here in the forums also helped: http://www.mobileread.com/forums/sho...d.php?t=190436
It turns out there is some incompatibility between SQLite and Samba. You can find a ton of posts about this if you search on 'sqlite cifs'. It looks like it is a form of file locking which is causing the problem. A full Microsoft client and server do no seem to have this problem. It seems to only occur if either the client or server is running Samba.
I've used the environment variable to move the DB and now the Calibre server updates properly when new books are added. The last step is to backup the metadata DB files now that they are no longer on the NAS.
Hope this helps someone else in the future.