[Off-Topic] folder permissions

This is a strange question I think, but I am convinced I am missing
something.

We have a 'template' file structure which has set permissions on the
different folders in the structure. Whenever we create a new job, we copy
this template folder structure into the job. However, all the permissions
get lost and all folders take on the permissions of the parent folder that
they are pulled into. Even though the 'inherit permissions from parent' is
unchecked in the template, when it is copied over it gets rechecked and we
have to go through and set all the permissions again.

Is there a way to keep the folder permissions set, no matter where the
folder is copied to?

Thanks for any feedback,

Sarah