I found an issue with flex while building doxygen-1.5.9 in cygwin 1.7. One obvious issue is that there is a newline inserted after every normal line in the .cpp output file, this will break code that needs multiple lines (like a multi line macro). The version of flex is 2.5.35 the same version I have used successfully in building doxygen using the cygwin 1.5* DLLs. My cygwin installation uses DOS/text file types.
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