Clearly *something* is not correct, or you wouldn't have this problem.

Double check the file on your server and make sure it has been updated the way you think it has. Check to see if Better Together shows as being installed in Admin->modules->order total. If you are running SEO URLs turn them off and triple check the id's of the products.

There is nothing organic in Better Together that would cause it to suddenly break down. Something has changed in your environment.