It is a Problem of the ownerchip.
If you have funplug installed, you can set the ownerchip via ssh:
chown -R youreuser /mnt/HD/HD_a2/yourefolder
chgrp -R youregroup /mnt/HD/HD_a2/yourefolder
chmod -R 777 /mnt/HD/HD_a2/yourefolder
change youreuser and youregroup to user and group.
and the /mnt/HD/HD_a2/yourefolder you must set also.
For a short test, you can open the webui and rightclick on an invisible folder.
Than select properties then mark all checkboxes. (read write execute)
but this is not recursive, but now you should see this folder via windows.(F5)
Maybe you "chmod 777" this on youre linux machine.
Or install funplug, its cool.