Apple did have a recall on the dual HD cable assembly. Make sure you have a newer one as they did have a shielding problem which could also mess your drives up in some cases.
I would bring the system back to Apple and have them replace the now defective HD and check the system out.
I would also get a temperature monitoring app to see whats happening that way as well.
Lastly, Do you have the system plugged into a surge protector and/or a UPS? If you did get hit with a large spike the surge suppressor might not be doing it's job. Best to get a new one. Does your UPS tell you anything? That would be a clue.