I think I have solved it now. The application passed an object from a third party library in a GAE session attribute. Sometimes when the object was retrieved from the session attribute it didn't work (often it worked but not always)! Now the application creates a new instance instead of passing it in a session attribute and so far it's working all the time. Something to do with the serialization/deserialization of the object put into the session perhaps, or that using an old instance sometimes failed and that a new instance is needed in this case.
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