Without seeing exactly what you are doing I can't properly  answer
your question but here are a few things to check that may lead you
to the problem.

Sharepoint respects NTFS permissions  so if the documents  are outside
of SPS then the permissions on the external documents will be
respected and if you don't have permission then you will not see.

It does sound though like your problem is within the Portal itself.
Ensure that you have assigned only those that you wish to have
access to Author or coordinate in the relevant areas. Everyone read
access for a shared area is fine but the Coordinators and Authors
are those that can do any changes.

Ensure that you havent accidentally added a group containing
everyone into a group with either author or coord permisions.

Also remember that the permissions like with a normal file system
filter down through the files if you select that option and it may
be that you have to go down and extra level and take off the user
parent permissions and thin out the Authors / coordinators.