I had the same problem, try one of
lexer-gcc-3.1.sh (should be in the root of the package)
or
http://lists.gnu.org/archive/html/lilypond-devel/2005-02/msg00015.html
and the following discussion:
http://lists.gnu.org/archive/html/lilypond-devel/2005-02/msg00057.html
Some versions of Flex generate code that some versions of gcc choke on.
Mark
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