Hi

bison is the GNU version of yacc.  It supports extra semantics and new 
functionality.  Without seeing the errors, I am unable to assist further.

flex (the "F"ast Lexer) is the GNU version of lex.

My wild guess is that the windows-compiled (cygwin?) version is perhaps updated 
to support the additional functionality that Bison/Flex support.

One such difference is the support of POSIX regexps, e.g.:
[:alnum:] versus the traditional [a-zA-Z0-9]

Hope this is of some benefit.  You could check the following site for a better 
treatment of the topic

http://dinosaur.compilertools.net/


dan.
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