Full path in the menu
I would try the following.

Take a backup of the database. Backup and Migrate makes this easy.

Make sure core and modules are up to date, especially Pathauto and Token.

Browse to admin/config/search/path/patterns, and set the path pattern to [node:menu-link:parents:join-path]/[node:menu-link].  Credit to Menu path in Pathauto.

Browse to admin/config/search/path and delete the bad aliases, or admin/config/search/path/delete_bulk and just delete all the content aliases.  Be careful here, and make sure you have a backup.

Spot check a few nodes, and make sure the "Generate automatic URL alias" is set.

Double check that the nodes have a menu entry set on the node edit page, and that the parent is correct.

Double check the menus and make sure that the links have the paths set to node/XXX.  You need to click the EDIT link to see this.

Browse to admin/config/search/path/update_bulk to create all of the aliases for the existing nodes.

Clear Drupal cache from admin/config/development/performance

That should work.