"ant javacc" in Windows/Cygwin generates files with wrong line endings (\r or \r\n instead of *Nix's \n).
I managed to get rid of those using perl -p -e 's/(\r\n|\n|\r)/\n/g'
Some useful info on line ending issues is in http://en.wikipedia.org/wiki/Newline
After wasting some time to get rid of those, I modified javacc-QueryParser build.xml task to take care of that.
So now QueryParser files created with "ant javacc" are fixed (if required) to have \n as line ends.
Should probably do that also for the other javacc targets: javacc-HTMLParser and javacc-StandardAnalyzer