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Well, asking the forum seemed like a good at time... Still, at least people now know what happens when you're an idiot.

And the answer is that the DMA request pin is dead. Fortunately, Linux has defaulted over to using PIO mode, and the data is coming off it nicely now. So while the disk is a bid dead its not a data loss situation (its backed up anyway, but restoring its a pain).

Never mind, just after I hit 'post' I found it here.

Well, we've just been dumb here. There are IDE drive cables that have pin 20 covered to stop them being put in upside-down. Well, we've gone and done just that (don't ask how, I can't even figure that one out right now), and while the drive appears to still be working I'd really appreciate it if...