Thanks you very much for the advices. I will work myself through the list.
The affected computer is my own. I just checked under the User Accounts in the control panel that I am "Administrator". For the SFC I ran the command prompt as an adminm (right click -> run as admin), but the computer wasn't in safe mode. What I find under "enable hidden admin account" seems to go further, I'll stick to that.
Could you share the online tools do you reccomend for the cleanup?
Versions... I have tried 1.8.5, 1.0.6, 1.0.5 r2. Is there one you would try out first or discourage me from using in this situation?