Pantone color issues while PDFing

The company I work for designs/publishes a magazine and have just been upgraded from CS2 to CS4. Since then, I've started having some problems when I PDF or print an ad. I'll receive an ad as a PDF and a component of their ad will be a Pantone color (typically logo). When I PDF the magazine page, the logo will change to another color. It's as if it doesn't recognize the color as CMYK. This also happens sometimes when I print. Any suggestions?

Some further clarification may be in order.
Spot colors ar not CMYK, though they might have a fairly close approximation. Most magazines don't offer spot color support, so everything must either be designed in CMYK, or converted. There are MANY spot colors that don't have good CMYK equivalents, and for those you will see a color shift after the conversion. Checking the "use Lab values" box will probably get you the closest possible match in a properly color managed workflow.

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