Yes, obvious bug. I have the exact same problem. I don't know why the geniuses at Canon could not understand your clearly written question.
The basic problem is that it is much more interesting for a developer to create a cute, sometimes cool feature like this, than it is for someone to write a dull, boring, settings option to turn the feature off. So they create the feature and don't bother to think that it may be a huge hassle for most people and nobody feels like writing the code to allow it to be turned off.
It is by far the most annoying thing with my multiple canoscan scanners. I can sometimes work around it by turning the image sideways. And almost always can fool the program by rotating to an angle that is neither zero nor 90 degrees. The scan comes out at that weird angle too, but compared to the option, it is really great.
BTW, the other horrible thing with all my Canoscan scanners is how every time there is a Windows Update, it is like playing Russian Roulette with your scanner. You never know what will work on the other side of the update, or if it will work at all.
