Hi there,
i'm afraid we are all experiencing the same issue; Doctopus does not work for documents or folders that must be shared; in the case of folders, the 'shift-z' seems to work (I did it yesterday, I manually placed Class Edit and Class View in my students folders, using shift-z). In the case of shared files, for teamwork and projects, ... I did not test it yet, but I suppose that the sharing permissions will be correct but the shared docs will not be placed within the team members' folders.
So, I look forward to a solution; in the meantime, I will 'survive' with manual arrangements.