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calibre 2.5 has a security update, it randomizes the internal seed used for generating hashmap keys. This means that any code that relies on iterating over the keys in a python dict in a fixed order will break.
Technically, it is broken anyway, since the python dict is not supposed to returns its keys in any well defined order.
I'm guessing something in that plugin indirectly relies on a fixed order iteration if the same column is used for different algorithms. That iteration order is now random, as it should be, leading to random results.
And note that a calibre update does not touch *anything* in the config folder. Updates only touch files inside the calibre installation directory.
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