Answers inline:
I was just wondering where you are saving the backups?
<BAM> NAS with a freshly formatted hard drive... Nothing on it to start with. The issue is 100% reproducible: all what I have to do is unlink the remote drive from windows (i.e: start fresh from windows perspective), format the NAS drive and relink for backup. <\BAM>
Could there be a situation where the missing files/folders were in a prior backup and had not changed?
<BAM> No, because I am starting fresh for both Windows and the NAS. What is bizarre is for both the C:\Users<USER> and D:\ Windows 10 is backing up the hidden folders but not the other (visible) subfolders. <\BAM>
I don't have that much experience with the File Backup setup but I have a link to music on a NAS and it gets skipped. Are the pictures on D: linked to your User Pictures folder and can you tell if they are being backed up that way?
<BAM> I am not aware of any shortcuts in my case, I did double check! The two folders on D:\ are NOT linked in any way to the Pictures folder under C:\Users<USER>... These two folders are standalone folders with subfolders and pictures.
Note that if I specifically ask for the subdirectories to be backed up (i.e: C:\Users<USER>\Documents, C:\Users<USER>\Pictures, C:\Users<USER>\Music, etc....) they DO get backed up as expected! But not when the parent directory (i.e: C:\Users<USER>) is selected!
Without understanding what is going on we CANNOT trust that the backup application is doing its job! What else could be missing!