After further research, the problem only exists for notes organized under sub-notebooks. Notes created directly under notebooks work fine.
Notebook1
Note1
Note2
Notebook2
Subnotebook
Note3
Note4
Notes1 and Note2 are sync’d and available on both machines. Notebook2 and its contents (Subnotebook, Note3 and Note4) do not even appear on the other machine even though both machines seem to have the same files.