Hello,
Have you read the post http://sevenspark.com/wordpress/menu-item-limit ? It explains what caused the issue. Because of the limit your WP can’t save all the menu items and just save the first part before the limit. Try to increase PHP max input vars limit to 8000 and restart Apache. If you search similar topics on our support forum you’ll see that you are not the one who faced this limit problem and solved this.
Regards