[Zubersoft]

It does appear that I misspoke - I used to require folders, but after feedback from users, I changed the logic with the cloud sync so that it will match the tablet. So if no subdirectories are used on the tablet, then no subdirectories are used in the cloud sync folder. This just depends on whether Settings->Storage->Create Subdirectory per Song is enabled. When the library is uploaded, the same logic is used for PDFs, images, etc as for audio files. 

Can you just clear out the contents of the sync folder, make sure "Create Subdirectory per Song" is set the way you want, sync to the folder and verify everything appears as you would expect after? If the library on your device has a mix of folders, you may want to consider creating a backup file, then restoring that same backup file, which will put all of the song files into the correct location (just make sure the "Restore To" dropdown is set to the MobileSheets Storage Location and you have the option enabled to let MobileSheets manage your files).

Mike