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I'm not sure entirely on what schematic you're using. Brendan showed me one recently but if it's the same there's a few things you could check:
On the DB9 connector for the motor:
Pin 5 - 12V - This would rule out problems with the internal power connection.
Pin 7 - 5V - This would rule out problems with the internal regulator.
Pin 9 is ground. Take care not to short between any of the pins as it doesn't look like the power supply has any decent short circuit protection.
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