Rob,
What has changed?
Do you see the red fill on screen, or only on export?
Have polygons been edited? Perhaps the geometry has been compromised - run repair geometry.
Are features selected, and your selection color is set to red?
Your output is Black and white in the one pdf, is your source all black and white, and the red fill is coming from nowhere?
Have you tried printing vs exporting to PDF?
If you export to image, does the red show?
Regards,
Jim