Problems with ps and pdf output

[Nathan Curry]

I got some problems worked out with my client's Lilypond installation, but I 
have a script that he runs that converts everything to pdf and ps, but there 
are errors:

1. .ps and .pdf are picking up the feta font (i.e. the music) but not the
markup.
2. .dvi is picking up the markup but only partially the feta font.

I execute the commands from the intended output directory. The commands I 
run are, for lilypond files:

/usr/bin/lilypond -V --include=/path/to/input/directory input_file

for lilypond-book files:

/usr/bin/lilypond-book -V --include=/path/to/input/directory input_file
/usr/bin/latex input_file
/usr/bin/dvips -Ppdf -u+lilypond -u+ec-mftrace input_file
/usr/bin/ps2pdf file.ps <http://file.ps>

I don't know what is going wrong. It seems like there might be an error in 
the conversion process, since the output is inconsistent across formats, but 
then again, direct lilypond output produces the same anomalies.
-Nathan