Sometimes VueScan's white balance algorithm doesn't cope well with unusual lighting. For instance, the light from a sunset will be adjusted so that the sky appears grey instead of orange and scans of flowers will appear less intense than they should.
The best approach to solving this is to change "Color|Color balance" from "White balance" to "Neutral". In addition, if you're scanning slides, make sure you've set "Device|Media type" to "Image".