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I think it would be the issue in the firmware, probably race conditions in the code that's writing to the memory cards, which would cause it to corrupt the data on the card only if certain timing conditions were met. Different card readers in different specimens of Cybook probably have different access times for various accesses, varying by microseconds of course, but that's why it would corrupt certain cards, or on certain readers, and wouldn't touch the other cards.
Writing to the card should be a part of underlying Linux system - perhaps Netronix is using Linux that is ages old, and didn't update its code even once since they first compiled the software together, and there are very old bugs in this code. All the more reason to let the users look at it...
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