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See the Cygwin64 port page for some info. See Trac 15015 for what is most likely your specific problem. The current maintainer, JP, will likely respond to emails about the Cygwin port quite rapidly.

I think that trying to use the system versions is (for now) a sure path for a descent into frustration. That is starting to change with things like lmonade but probably not doable on Cygwin yet (ever?).