I thought I could use UNIX notation in Cygwin but I see I cannot. oops.
Wrong again.
Cygwin is not a tool that magically wanders over all your installed applications (e.g. Office) and somehow makes them "Unix-aware".
Applications compiled against cygwin libraries can use POSIX conventions for files and paths (provided they are configured to do so - there's also software logic to be considered).
Java, however, is a plain old native Windows program. It will understand forward-slashes (because that comes for free with the Windows API), but paths have to be ";"-separated, and of course, it won't understand Cygwin mount points (e.g. you can't pass in "/usr/some/path" to Java and have it figure out that you really meant "c:/cygwin/some/path").
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