I have created new taxonomies and added them to a WPAdverts custom post type. Whenever I add new values either through the backend or the frontend, Meta Box adds new taxonomy values as numbers and uses them for the CPT entry. For example, I added 'WordPress' as a category, but Meta Box uses the newly created '808' as the category. Do you have any idea why this happens?
Can you please share some screenshots of the issue on your site? And export the custom taxonomy on your site to a JSON file, I will import it to my local site check this issue.