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On Jenkins 1.575, working against Windows Server 2012, setting the JDK in Jenkins provides the option to input the JAVA_HOME variable, and that worked around the issue for me.
This might be what you were referring to as having it set twice, but given that it seems to completely ignore JAVA_HOME on the clients (even though it reports that correctly with the script console) it doesn't seem to cause any issues.
Here were my steps:
such as C:\Progra~2\Java\jdk1.7.0_67 where Proga~2 resolves to Program Files (x86)