The meta box checks for the edit_post capability when saving the data. If the user doesn’t have it it reverts back to the old settings. This capability is by default added to admins, editors and authors unless a plugin has tampered with the default capabilities. For custom post types it checks for the corresponding capability (i.e. edit_page for pages edit_product for WooCommerce products and so on). I doubt it inherently related to the database, more likely it’s an issue with a plugin tampering with the capabilities or post saving.