What version of Internet Explorer is installed, you don't need to be using it, but McAfee does?
You applied the fix from the FAQ ? Maybe try it again?
Scans can sometimes trip due to hard disk-read errors. Here's a Tutorial on how to check the disk for errors: CHKDSK - Check a Drive for Errors in Windows 8
If all that doesn't help I would contact Technical Support by phone or online chat, it's free of charge and linked below.
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I will try chkdsk and possibly SFC later (got a bit on at the moment).
Do you think it will be safe to apply the fix twice?
MVT has not found anything, it is all green and is updating OK.
One thing was strange was that during the 1st scan (when the issue reappeared) vulnerability scanner ran at the same time is that normal?
I don't think it would harm anything to try the fix again. Regarding Vulnerability Scanner, I guess it was just coincidence that it was run at the same time. You should maybe turn off it's schedule in PC & Home Network Tools.