Are the compiled versions of the lexer .l and parser .y files
included in the LilyPond distribution? If not, it is probably prudent
to include those, because installations tend to vary a lot with
respect to which lexer/parser generators, and their versions, are
installed.
lily/parser.yy, lily/lexer.ll in the source distribution.
Hans, if this had been an issue, it would have been taken care
of a long time ago. Remember that LilyPond has existed for almost
9 years now. Actually, there are several other version dependencies
that have caused much more problems over the years.