Save as EPS in CS3

I work for a government agency that currently creates their graphics in Illustrator, exports them as EPS, and then places the graphics into MS Word templates for production. Sometimes, however, we have complicated graphics that use layerd transparencies. When these are saved as EPS files and converted to PDFs, white boxes and lines appear around the transparent objects. I believe it might be because the Transparency is flattened when you save as EPS, and this causes the lines to appaer (Saving out of AI directly to a PDF does not generate the white lines).
My question: Is there any way to save from Illustrator to EPS WITHOUT flattening the transparency? Because of the current workflow of the agency, the graphics need to be in EPS format before being placed into the Word reports. We are upgrading to CS4 in the near future....might there be a way to do this in the new version? Any input is greatly appreciated! Thank you!
Meredith

the best solution its to save for web and devices and choose "png-24" . I use EPS only to interchange logotypes or simple draws with other designers

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