EDIT/UPDATE: This Topic has been cleaned up/condensed to show only relevant info.
You would add an AutoRestore folder Exclude rule for the languages folder or the languages/themes folder using the Exclude wp-content Folders tool.
1. Turn Off AutoRestore.
2. Type a label/description in the label/description text box and type/enter: languages in the folder exclude text box.
3. Click buttons 1, 2 and 3 in order.
4. Note: this step is probably not necessary. Click the wp-content Files Backup Files buttons. This will create the languages folder in AutoRestore backup if it does not actually really exist.
5. Turn On AutoRestore.
6. Restore all of the language files from Quarantine.
Notes: Logical guess: I think what may be happening is that WordPress is creating a new folder under the languages folder. This is probably something new that WP is doing. So by clicking the wp-content Files Backup Files button you are creating the same identical new folder under your AutoRestore backup folders and files. Once you do that then you should be able to restore the files.