To share what my solution was for now, I ran a system restore to a point where the user knew that they scanned a document, and all is working except that I need to keep an eye on what updates are applied in the next couple of days because the problem may have come there, although most likely is was a corrupt profile.
It seems to be a problem in the profile.
One option could be to <a href=”http://www.microsoft.com/downloads/details.aspx?familyid=901a9b95-6063-4462-8150-360394e98e1e&displaylang=en”>delete the profile</a>, so a new one is created the next time the user logs in (if it is a domain account).
P.s Remember to bakcup relevant profile data before deleting the profile.
Goto Documents/Scan to PDF/Configure Presets and check the top option to ensure it shows your scanner/printer.