Power supply could be the answer, but having two HDDs close together is not a good idea unless you mount them in chassis with front fans that suck air in over them. Hot stale air can build up around them and het is a great HDD killer.

The Clone machine sounds as if it has a corrupt partition. Get the diagnostic tool from the manufacturer's website and run that.

The fact that you are having these problems in spates, does suggest a mains power supply problem. As suggested you should use surge protection. Have you had any other "strange" symptoms, such as an increase in blown lightbulbs or the like?

Cheers