Windows System Variable with SSH

[dnbphysicist <robhyx at GMAIL dot COM>]

We have an open ssh client installed on one of our Windows 2003 servers, and
are able to login in and everything, but when issuing commands some the
System Paths (which are in .bat files on the server) such as %JAVA_HOME% are
not recognized. I assume this is because Cygwin does not know how to
interpret the % signs. Is there anyway to get Cygwin to recognize the system
variables with the % signs around them.
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