Hello Ben,
Does the workaround pointed out later in the thread you're
responding to (from the last paragraph of a very long 'Note'
section of ?pdf) help?
Well, I did not try to edit my fonts.conf but I feel this is not a PDF issue. I have no problem to have greek letters correctly rendered in Ubuntu 10.04 (with LaTeX, or OpenOffice Math for instance with a PDF export). This only appears in R plots.

Note that other symbols do not render well too. I put a PDF output of demo(plotmath) here:

http://yvonnick.noel.free.fr/wrongsymbolsinubuntu.pdf

Thank you.

Yvonnick

> sessionInfo()
R version 2.11.0 (2010-04-22)
i486-pc-linux-gnu

locale:
 [1] LC_CTYPE=fr_FR.utf8       LC_NUMERIC=C
 [3] LC_TIME=fr_FR.utf8        LC_COLLATE=fr_FR.utf8
 [5] LC_MONETARY=C             LC_MESSAGES=fr_FR.utf8
 [7] LC_PAPER=fr_FR.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

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