I had a similar problem when I upgraded to 2.4 lilypond under cygwin.
Turned out that there was an environment variable problem. I added this to
my .bashrc file:
export TEXMF='{/usr/share/lilypond/2.4.2,/usr/share/texmf}'
and lilypond was happy.
Interestingly, lilypond worked just fine when I ran a plain bash shell
without X. I only saw the problem when I ran lilypond in a xterm.
- James
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