There does seem to be a design problem with this model of drive Read this Link and others have experienced the noise you describe which only happens if the drive is allowed to spin down to a stop before re-starting. Hence it is OK after a re-boot or when running but does not like starting from standstill. Personally I would clone everything onto a new hard drive and replace it as soon as possible. You could always put the old one in a caddy and use it for back-up (although I am not sure I would trust if for very long).
Sony Vaio Z Canvas release date, price and specs: Another Surface Pro rival but for the US