Permission Denied on Arduino serial stream
Don't use Cygwin. Seriously. I've been trying it for the last 15 years, and it just isn't a reliable way to write working software. The translation layer is just too fragile. I can't say for sure that this is a Cygwin problem, but that's the most obvious problem in the setup you descibe.

If you need UNIX, use Linux or BSD.

If you need Windows, use Visual Studio Express, which is free, and use the Win32 or .NET APIs.

And this sounds a lot like a software question, rather than an electronics question!