If I understand your issue correctly, I might recommend you establish a common workgroup folder structure for everyone to be able to contribute. Individual user's folders seem to have that issue of being protected from anyone else. It has been my experience that they can be given wide permissions for everyone, but as you say, when something is changed/added. it seems to implicitly protect that form that moment on and anyone accessing it needs to have permissions explicitly re-entered. Obviously not a viable solution. I don't know if that characteristic is a bug, oversight or a "feature" of unix-based file systems.
So what I did was create a workgroup with a common folder. Go under "Groups" on the main Server bar under "Accounts" and you will see the ability to crate a group, assign users and create a shared folder for that group. That seemed to work best for me. See if that works for you.