Final followup.
I am convinced the classloader / "class unloading process during redeployment" that is run when the deployment is made to a running instance is failing to load the newly deployed war file properly.
When the instance is running while the deployment from the das happens, failure happens fairly often with various bad results as seen above (exceptions of corrupted xml or war files, general hanging or core dump of the glassfish instance).
When we shutdown the instance, deploy from the das, and start the instance up again, the deployment works 100% of the time.
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