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Given that the problem seems to be in the deserialization of those files, I was thinking that given the files, and your knowledge of the code base, you could run them through the deserialization process and hopefully reproduce the problem. Not the case?
I tried to trace through the deserialization process with my debugger attached to the affected machine but, in the time I had, I was not able to get my head around the deserialization code sufficient to understand what was going on.
Would a comprehensive list of all plugins installed on the box help? A copy of its config.xml file? Not sure what are the relevant details.