After two days of random not-working-ness I finally checked my hard drive which had some minor issues that Disk Utilities repaired - from the OSX System Install disk - not the drive itself. Then I "repaired permissions" again (first thing I do when things are acting odd) and restarted everything.
Upon starting Live it still was not seeing the Korg, though it was clearly in my MIDI Devices screen. So i turned the Korg off, then on again while Live was open. Wouldn't you know it... now it's there again! And my MIDI preferences screen now looks correct - showing all the INs and OUTs of the microKontrol.
I'm sure I had done this before - but perhaps whatever was wrong with my home-drive was messing up how the drivers were loading. Very odd, indeed.
