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This is a http://cygwin.com/acronyms#WAG, but have you got CYGWIN=server set in your environment, and are you running the cygserver? That's a pretty common cause of "Bad system call" errors.
Of course, I would already have known the answer to those two questions if you had sent your cygcheck output as an attachment, like it says at http://cygwin.com/problems.html !
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