SOLUTION
This is a scanning directory rights issue. The default directory that the scanner tries to save scanned documents to is Documents. For some reason the owner of the Documents folder when you upgrade to Windows 10 doesn't always transfer to your login properly.
Here is how I solved my issue -
1. On the Documents root folder, right click, select properties, select security tab.
2. Click Advanced
3. The window that pops up should show the current owner. It will probably look correct. Click "Change." The "Select User or Group" pop up box appears.
4. In the text box, type in your current user name (you should be an admin), and hit the "Check Names" button. Your name will be replaced with the "official" system name (i.e.,preceded by computer name and back slash).
5. Click OK
6. The box disappears, sending you back to the Advanced Security Settings window.
7. A new tick box appears below owner, with the text "Replace owner on subcontainers and objects" Select this tick box.
8. I also selected the tick box "Replace all child object permission entries with inheritable permission entries from this object", but I think I had to run this twice - once with this box ticked and once without.
9. Hit apply.
I would also advise going into the Canon IJ Scan Utility and click Settings. Go to the second tab (looks like a hard drive with an arrow coming out of it). Now change the 'Save in' location for each of the 4 options. I created a 'Scanned Documents' folder under Documents so they all don't just drop into the root of Documents. I changed the Photo scans into the Pictures directory.
Let me know how you get on.
