If the color of your slide background in your published output is not the same as the slide color you have specified in PowerPoint, then the issue may be related to the background image in your slide master.
If you want to use an image with a transparent background in your Presenter ’09 presentation, the image you import into PowerPoint must already have transparency applied. The transparency cannot be applied via PowerPoint. The slide background color may be visible through the transparent areas of the image.
The work-around to get the correct color on the slide is to duplicate the applied design and select the desired background color, then apply this design to the slide.