I am sure we can help you with this. What pdf setting did you use, smallest file size?
Set color to "No Conversion", this will keep in cmyk and not go to RGB.
If this does not help, let us know about your blending modes, and also make sure overprint preview in on in Illustrator, and in acrobat. Not sure what preview does with overprints.
Hi Mike, thanks for the help but unfortunately that didn't work. It's really strange. When I save for web, the correct colours come up - it just doesn't seem to get the correct colours when I save to PDF and it's driving me nuts!
Any other ideas? All help is appreciated.