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Thanks for looking further. I can see how the filler fields you added will now trap the error (even with the fall-back 'XML serialisations are the same' object comparison), and why it passed previously. Your description of the problem would also explain why leaving only one array/collection implicit would avoid the problem.
Do you currently know the root cause (and hence why it's intermittent)? Is this likely to be a high priority fix?
P.S. Does this type of problem (XML serialisation the same even when objects not the same) suggest that, in general, equals methods in test classes should ideally always be coded? Obviously there's effort in coding them though...