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.