The jnlp file can include property elements in the resources block:
...
    <property name="some.prop.name" value="some.value"/>
and Java Web Start will set these as system properties if the code in the same jnlp file would be granted permission to set these properties.

but if a policy file is present, even granting everything all-permission, then AppPolicy.addPermission() will still not set the property, and it will call ignoredException with a new AccessControlException(...).

If the first jar in the jnlp file has access to write the property, Java Web Start should write the properety and not log the exception.