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I added a comment under JENKINS-20364, but it is somewhat relevant also for this issue, so I'm copying parts of it here.
Assuming that the fix made here actually works (otherwise it would have been re-opened long ago), my second comment can be ignored – 64bit JVM running on 64bit Windows looking up "HKEY..WARE\Wow6432Node\Cygwin\setup" probably works. The problem is that this fix does not work for 32bit JVM running on 64bit Windows (see my comment on JENKINS-20364 for details).
Useful reading:
http://windowsitpro.com/systems-management/whats-wow6432node-under-hkeylocalmachinesoftware-registry-subkey
http://msdn.microsoft.com/en-us/library/windows/desktop/aa384129(v=vs.85).aspx