Win10: Movie collection on NAS (via SMB), random folders missing in Kodi

Hi there!

I guess this problem is related to Windows, but I am not sure – it might also be OS independent.
This is about missing folders on a SMB share – they exist, but Kodi doesn’t seem to be able to seen them.

Setup:
Windows 10
Kodi 17 Beta 5 – currently, but I’ve had the problem (for series; don’t know if movies, too) since Kodi 16, at least
Movies on a Synology NAS, shared via SMB, mounted in drive Z in Windows
Movies (nfo, images, and folder/file names) are managed with Ember Media Manager, if that matters; Kodi source is set to “Local information only”

Problem:
Some Movies are missing from the database. Upon further investigation I noticed that in “Videos” -> “Files” -> “Z:” also doesn’t show the folder – same with the Kodi file manager. From within Kodi, it looks as if the folders wouldn’t exist.
The diskstation web frontend and Windows Explorer, however, display the folders and I can play the movies with VLC.
Explorer shows 1656 entries, Kodi file manager shows 1542 entries – 114 entries or 7% missing.
For series, it’s even worse, with only 14 of 27 folders displayed. It doesn’t seem, however, as if files or subfolders are missing – all series that are there are complete.

Thoughts:
I have read two threads here that describe exactly the same, but the cause seems to be different here:
One thread (can’t find it right now) was about a virus scanner (could have been Avast, but I’m not sure) – I am using Avira, and have tested disabling it. Nothing changed.
This thread seems to fit very well, but I have since enabled Samba3 in the diskstation settings. Nothing changed.
I checked permissions on the NAS – my test folder is owned by the same user and has the same permissions as other folders that do show up.
There are no special characters in the name of the folder.

Is Kodi using plain windows file access for the files on Z: or does it know it’s an SMB share?
Do you have any thoughts or ideas how to debug (or even solve Smile) this?

Imanuel