Hi Christopher, I know I've informed you of the following in our support conversation but i'll update this thread too in case anyone else has a similar issue.
Stablebit's software is working great of course, and the issue seems with my config. I was thinking it's an incompatibility with the 6Tb Red Drive, and my HP Microserver. But something you said sparked a light in my head, which was about the controller i'm using. I'd been using the generic windows SATA controller. This is because HP doesn't provide drivers for Windows 8 for the HP Microserver (N54L). But i saw from other people's configurations that they seemed to be using an AMD Sata Controller driver. So i searched the net and eventually found the AMD driver compatible with windows 8 and installed that. Although the disk disappeared after restarting, a full power down and on again got it back. And so far i've done a complete scan of the disk, this time without any errors. Since that's the first time the scan has completed without errors for that disk i am now working on the assumption that the SATA driver was the problem. I'm doing more tests but with a bit of luck i hope it's solved.
Thank you so much for suggesting the controller drivers could be an issue as i think i never would have thought of that. Shame HP don't support more systems, though yes i expect Windows 8 isn't the first choice of OS for it.
Thanks again for the advice and ideas, it may well have saved the day for me