I am using Windows 10, and downloaded the latest MF Scan Utility from Canon's website. Your post got me thinking about utility versions, and I found the install CD (which I often don't use because it's out of date by the time I get it). I uninstalled...
I have this issue as well. Using the MF Scan utility, there is no setting for selecting a source. (Screenshot attached) Not sure where to go from here.