I've decided to image, fabs and N&P.
The whole computer has issues with file corruption, permissions, programs not loading and giving errors, so I think BD has been affected as well.
I'm probably being a bit harsh on BD because we all know how good it is.
Emsisoft use their engine as well, so I think if BD was working correctly the "detected items" may have been dealt with by BD anyway.
Even though Bitdefender said it was up-to-date, the signature files were from several months ago. Emsisoft use the same definition files so they should be similar date - if not exactly the same.
Your right about the settings, some that I changed were changed back after a reboot, so maybe one of the infections was fooling with it?
There are multiple other issues as well so I think the N&P is prudent.