When the site is originally set up, the /database folder is set up by default as a READ-WRITE folder. When the permissions change to READ-ONLY, usually it means that the /database folder has been removed and replaced, most likely while content was being published.
Unfortunatly, when /database is removed and replaced, the folder loses its custom permissions, and instead of being writable, the new replacement folder inherits the read only setting of the parent folder.
This usually occurs during a global publish or site update operation. Many FTP clients, FrontPage and other publishing tools often remove and replace folders during a global update. In the case of /database, its best to only replace the contents of the folder, not the folder itself. When publishing, you may need to verify that /database and its contents are not being automatically replaced by your publishing software.