After commenting-out all code related to FileIO and the microSD card, it started working again. Slowly re-introducing each line has shown me that my arduino had run out of memory - I had created a global array of ints to buffer the colour data coming from Processing. I've reduced that array's size by half, and it is now working robustly!
I think when the arduino was powered up, it would attempt to open the Console, but then it would reset itself (because of running out of memory??), resulting in the 'Connection closed by foreign host' message.
Sorry for the false alarm!
Best,
Aran