Spot Color mismatches between EPS and PDF files

Recently I created a file in Illustrator CS6 with several Pantone color swatches. I used the CMYK color mode set to the Coated GRACoL 2006 color space. I saved the file as an EPS and we printed our test samples on our large format printer. After reviewing the print I saw the colors were off. The grey color showed up green.I then opened up the exact same EPS file and simply saved it as a PDF. We ran the PDF on the same printer, using the same material and profile and the color was completely different. This time the grey colors came out grey (correctly). We tested this twice and came up witht he same color differences between the EPS files and the PDF files. Why would an Illustrator file produce 2 different colors if saved as a PDF versus an EPS?
Also, I sent these files to another prepress person in our company and he printed them on our proofing printer. The EPS printed slightly differently than the PDF. He then opened the PDF file in Acrobat and saved it out of Acrobat as an EPS. After this, he printed the new EPS file created from Acrobat and it printed the exact same as the PDF file (correctly).
This leads me to believe that the problem is in the way Illustrator saves EPS files. Has anyone else seen this problem?
Thanks for any and all help with this very perplexing issue.

I will speak from CS3.
The current PDF format if 1.7 exported out of Photoshop supports vector elements as independent objects, but you can't edit them correctly out of Acrobat because Photoshop reads the data as a flat file and drops the vector data. Basically the workflow is not finished being developed. Also, Transparency is broken within the PDF file format at this time. It will support Spots though correctly.
PSD and TIF support Transparency and Spots, but vector objects are rasterized due Acrobat reading the flat version of the file.
When Photoshop wrote its own PDF format and not the corporate PDF flavor that we now have, PDF's would support Transparency correctly.
I would assume that Transparency and vector objects would be addressed in the next release, but that is to be seen.
There is no best practice except don't do it.

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