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.]
The Smell of Molten Projects in the Morning 
Hmm most of the time i pull the usb cable because its just wrong ;-) that it powers the fan. But this sounds like a solution. Could u post a bit larger view of the arduino board so that i know where to look for (i usually do not cut into hardware). Its a bit uncleare to me (noob… yes i know and i am)
It’s pretty straightforward. That picture of the Arduino Mega 2560 shows the power input as the rightmost pin in the lower left block. Match the Mega up with that picture of the Motherboard and you’ll find it’s right next to J4, the leftmost RS-485 connector (which has no actual connector, it’s just a set of holes in the board).
Flip the Motherboard over and you’ll see a trace angling away from that pin; use a good light because it’s hard to see under the black solder mask. Carve a hunk out of it, glop some glue / nail polish on the wound, let it cure, scrape the solder mask off the stub ends, and solder the diode in place.
It’ll take you five minutes after you work up enough courage to do it!
Thnx for the info. When i am adding my stepstruder i will make this mod ;-)