CrossRoads:
You also have to power the board when using it, the MKii only senses the voltage on the ICSP header, it does not provide power.
That could be very bad if it happened. With nothing on the +5 line the power could be getting in through one of the I/O pins, in which case it will switch on/off as you send data. Corruption will surely follow...
I assume another USB cable to the Arduino board would fix this.