I presume you have the latest driver version:
9000F Scanner Driver Ver. 16.0.3 (Windows 7/7 x64/Vista/Vista64/XP/2000)
The other thing is, are there any other twain devices that show up when you have the canon software running? When I installed my Canon multifunction printer, the scanner part wouldn't work until I deleted the other twain devices, which is a bloody nuisance as I cant then use them.