Here is the output: kpsewhich --expand-var='$TEXMF' {/home/ben/.texlive2008/texmf-config,/home/ben/.texlive2008/texmf-var,/home/ben/texmf,!!/usr/local/texlive/2008/texmf-config,!!/usr/local/texlive/2008/texmf-var,!!/usr/local/texlive/2008/texmf,!!/usr/local/texlive/2008/../texmf-local,!!/usr/local/texlive/2008/texmf-dist} and kpsewhere context.tex /usr/local/texlive/2008/../texmf-local/tex/context/base/context.tex /usr/local/texlive/2008/texmf-dist/tex/context/base/context.tex but it seems that it's just OK.
The problem seems to be the order in which TeX searches and uses the various TEXMF trees. Can you post the output of
kpsewhich --expand-var='$TEXMF'
and of
kpsewhere context.tex
Thomas
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