Bit of a far-flung theory, but I think it might have been a deliberate ploy to cover their tracks and keep their identity a mystery.  If it was someone closely connected to Unix development, but they didn't want people to connect the dots and discover they started Bitcoin, what better way to do it than to make the first version Windows-only?  Secure in the knowledge that if it was successful, it wouldn't take long for Bitcoin to migrate back to Unix, the spiritual home of open source.  Never underestimate Satoshi's brilliance and forward-thinking.