I think I found the answer here:
http://www.curlybrace.com/words/2010/12/17/console-and-cygwin-dont-show-all-files-on-64-bit-windows/

Quote:
This is because Cygwin bash and Console are 32-bit applications, and I'm
running 64-bit Windows. With filesystem virtualization on Windows, when
a 32-bit process attempts to access %SYSTEMROOT%\System32, it is
redirected to %SYSTEMROOT%\SYSWOW64. Ironically named, System32 contains
64-bit applications, while SYSWOW64 contains 32-bit applications.

These give the same version:
Win 7 DOS prompt: \Windows\SysWOW64\java -version
Cygwin prompt: /cygdrive/c/Windows/System32/java -version

-------- Original Message --------
Subject:        java -version different on Win vs Cygwin
Date:   Thu, 22 Mar 2012 09:30:45 -0500
From:   Pete Brunet <peter.bru...@oracle.com>
Reply-To:       peter.bru...@oracle.com
To:     build-dev <build-dev@openjdk.java.net>



I get different versions when I do the following.  Why?

Win 7 DOS prompt: \Windows\System32\java -version
Cygwin prompt: /cygdrive/c/Windows/System32/java -version

Is that java.exe a stub that routes to a different java.exe?  How do I
control which java is activated?

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