I am having the same problem, but my problem does not show
up badly until I convert the pdf to cmyk. It seems like
2002 worked but not this latest version.  I had a client
who needed a pantone purple. When I converted it to pdf
and then converted that to cmyk the colors were way off. I
had to pull out my pantone book with the cmyk values and
remap them from enfocus. The pictures are all converting
badly. The files I get come in as rgb and the pics are
embedded. It seems I get the same result if I leave the
pub file as cmyk or rgb before I print to pdf.
I have tried printing out the file to seps, but what a
pain to work with. I paid 300+ for seps to comp and it
works on all files but publisher.

I have had better luck with power point and word in this
area.