on admin/modules.php it is possible to hide modules. If this is done with modules of which instances exist in the courses then that has unwanted effects. For example the icon for that module will show up in the Activities block for the course but without the module's name after it. In Moodle 1.5 this also generates notices.
When one later makes the module visible again then ALL instances of that module are made visible, even those that the teacher had made hidden.
I think hiding of modules should simply be prohibited if there are already instances of that module.