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This is not perhaps a technically expert solution but I would uninstall everything, then bring them up again one by one, making sure that each drive works alone on each channel and on each cable, both as master and slave. Boring, but I reckon you would find out whether the problem is cable, drive (including master/slave/CS settings), or something else. Once you find the problem and can replicate it at will, solving it shouldn't be too difficult.
Hope this helps.
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