Calling node delete (node_delete_multiple) is not deleting all comments from database
you should check the watchdog table to see if there are any errors. The function calls comment_delete_multiple and with in that functions deletes all the replies as well. 

If there was any error during this process it would rollback to a specific point in this case I guess it would be during the delete process of child comments. Tne information would be stored in the watchdog table with type set to comment. This would give you a hint as to why it was not deleted.