It turns out the problem was in the AMConfig.properties file. This file had a bad directory setting for: com.iplanet.services.debug.directory. This caused an error to be written each time it could not write to the debug directory. It was further compounded because the property: com.iplanet.am.session.client.polling.enable was set to true. So every time it polled and failed to write to the debug logs it would send out a bunch of log messages to the glass fish log.
The solution was to fix the directory and then to set polling to false.
[Message sent by forum member 'leswestberg' (les.westberg_at_agilex.com)]
http://forums.java.net/jive/thread.jspa?messageID=362478