The Arduino Mega 2650 board used in the Thing-O-Matic gets its power from the +12 V ATX supply plugged into the TOM Motherboard. It will also automagically switch to +5 V from the USB connection when the +12 V external power Goes Away.
Come to find out that the Foxconn Atom I’m using doesn’t shut off the power to the USB ports when it’s “turned off”. That keeps the Arduino alive and, by a quirk of the circuitry, backfeeds +5 V into the +12 V supply, which makes its way back to the ATX power supply and keeps the fan running. Slowly, but it’s ticking over in there.
Rather than keep unplugging the USB cable, I added a diode in series with the Motherboard +12 V trace going to the Arduino connector:
The orange stuff is nail polish rejected by my Shop Assistant, which covers a slit gouged in the +12 V trace. The diode bridges the gouge and passes current only into the Arduino.
Any diode will do, as the next step in the +12 V supply chain is that poor overworked Arduino regulator responsible for shaving it down to +5 V. I used a good old 1N4001 and it’s perfectly happy.
[Update: the Arduino will remain powered up overnight, even with everything else turned off. When you turn the Thing-O-Matic on the next morning, pop the Reset button to get the Arduino’s attention.]