For a file, when you remove the inheritance of permissions from the parent space, you can not see that file. A user in the group of EDF_Pricer+_MOA can't see the file. Yet the permissions from the parent space and file are the same.
At first sight when I add permissions from a script that creates problems, as if he knew the rights that I propose.
For example in my script I do: document.setPermission ( "Delete", "GroupA"); He adds much to my doc right, but in reality I think he knows no right "Delete". I tested with "Collaborator" it is the same.
When I do the same thing with a user it works. There is a difference between a script and a user to set the permissions.