Thanks,
After doing some research into HTTPOnly itself and specifically in the Glassfish realm I discovered that it is enabled as a default in GF 3.1. I used the information at this site:
http://java.net/jira/browse/GLASSFISH-15730Specifically:
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HttpOnly is set to true by default for security reason.
If the the app does not have a cookie-config in the web.xml, then it can overridden by a default value in default-web.xml by
adding the following:
<session-config>
<cookie-config>
<http-only>false</http-only>
</cookie-config>
</session-config>
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This seems to work, no more issues with CSRF Security, however, maybe better option would be to extract the .war file and create the setting in the subsonic app itself and then re-packaging it so as not to enable that for the entire GF domain.