Your mileage may vary, but this is how I scan with Canon's software (MP Navigator EX 2.0)...
Open program, click "photos/documents"
check the box "use the scanner driver", then click "open scanner driver" button
Once the program opens I click on the "advanced tab"
Under "output settings" I set the DPI to 300.
Under "image settings" I only turn Descreen to "on"
(everything else under this category is either "off" or "none")
In the lower left, I click "preferences", then click the "color settings" tab
I change it from "recommended" to "color matching" and use the settings:
Source: Canoscan 5600 Reflective
Target: sRGB iEC61966-2.1
I leave the "monitor" box checked, then click "OK"
I will typically do a preview to be sure the card is straight, etc., then I scan
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