Hi, you mean the color of some images or the color of text? For the images this happens because they are compressed a little, have you tried using a higher resolution for conversion (in its Printing Preferences window there's a Resolution drop-down)?
I am having the same problem. I have a Word 2003 doc with a large text box with a tan background. When it gets converted the background is a blue/grey. I tried changing the resolution from 300 to 600 to no avail. I am running WinXP. My doPDF is version 6.1-281.