The default settings of the content structure menu have been changed. For more info, please read this bug report: http://ez.no/community/bugs/new_default_contentstructuremenu_ini_settings_break_existing_configurations_unnecessarily
To avoid future load problems on large content structures we decided show only the most important classes in the content structure. Usually it is enough show only folders till 2 second level, this can speed up admin page load slightly. On small websites I can agree that current settings are too strict and you can show all classes. For me this is not a bug, it is undocumented feature which comes with 3.8.
