Anyway, earlier I opened up the side of Nyx to blow out some of the dust, and having put the side panel back on the card reader has started working again. I swear I've not touched any of the cabling for it! Apparently I can fix my computer just by taking the side off and putting it back on.
This all reminds me a bit of one time in the Brighton house where I'd done some upgrade or other on Achilles/Hector (my previous system), and after putting it all back together it refused to start. I checked all the cables were connected and everything was seated properly and it still failed to boot. So in a fit of desperation I stripped the whole thing down, put it all back together exactly the same... and it started fine. I blame Nik's presence for that - it was well known in the Brighton house that he could break electronics just by looking at them.