Seems to be a problem with folders that are also synchronized to OneDrive - there the subfolders are no longer included. If I copy the same folder including the subfolders to my local harddrive and make a new folder pair from there, Synchtoy is working correctly.
From the original folder located in OneDrive it will only synch the files found directly in the folder, but disregard any subfolders therein.
Checked with Synchronize, Echo and Contribute - also set all folders manually to 'available offline' in OneDrive.