Well as no one is interested in reading anything that long I've got rid of it all. I have managed (for those who are interested) to hopefully sort the problem by using the other SATA controller on the board. I thought the drive or cable might be faulty so I tried another drive that I had spare (same make and model), strangely using the VIA SATA controller it didn't detect it, something about the bios not present. It worked fine on other computers so I switched to Promise RAID controller (which detected the newer drive) but I carried on using the original drive. The problems seem to have gone now, but I may create another thread about chkdsk errors anyways.