Motherboard communication issues

Hi there, at London Hackspace we've been trying to get some reprap gen3 boards working. We wired up and powered on a motor board, connected to an unpowered motherboard: the motor locked up. Disconnected from the motherboard, only the green light would come on. When we plugged the motherboard in via a USB-serial cable, the motor freed. But it wouldn't respond to serial commands sent from the reprap software. Upon investigating the output of the boards using the arduino software, we found that one was repeatedly transmitting "startstartstart" back to the computer, and the others were silent.
Does anyone know what the problem might be? We've been puzzling about this since about midnight...

The stepper boards have an active low enable signal. When the motherboard was un-powered it probably dragged it low enabling the motors. When disconnected or with the motherboard powered the enable was high turning off the motors. So it seems the steppers are behaving, the problem is the Arduino is continually resetting. Check that the 5V line on the motherboard is stable at 5V.

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[www.hydraraptor.blogspot.com]

The +5v was coming from a USB port, I can't think why it'd be unstable...