Folks,

I've re-opened this thread to post an update and a solution in the hope that it may help others in the future. A few weeks after my last post the system started to show the problems again with the disk disappearing. I tried numerous things, including running chkdsk on the 1Tb drive (took over 24 hours). Yet still the problems persisted, I even upgraded the motherboard and processor in an attempt to see if that would cure the problem.

In the end the problem turned out to be an extension to Windows explorer which under the original hardware caused the disk to drop out. Under the new hardware the disk just became inaccessible for an extended period. Using a combination of ProcessExplorer and the Resource monitor from Task Manager I was able to identify the problematic addin, in my case the problem was caused by Acronis's Shell Extension (tishell64.dll). Using ShellEXView I was able to disable the extension and the problem vanished. Enable the extension and its back.

I'll leave this opeen for a few days in case there are any questions, and then I'll mark it as solved.

M.