We have come across this issue as well. ezPublish is designed so that the section_id is associated with the object table:ezcontentobject) and not the object tree (table:ezcontentobject_tree). So when an object it copied to a new part of the tree the section ID remains the same (that of the "main" object")
Have contacted ezpublish over this and they will be supporting nodes and subtrees in the permission system in the next release.
I'm not that comfortable with permissions/roles being combined with page layout in the way it is currently done.
