Hello,
Which image are you and your people using?
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uname -a <<<< use this command to find out
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The BBB and other variations run on another battery supply. Do not try to run both the Motor Bridge Cape and BBB off the same power supply.
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The BBB runs off of 5v or 3.3v only. You can run your Motor Bridge Cape off a 12v 1.3 Ah lead acid battery.
Seth
P.S. If this is not the issue, please contact me. You may have to set up config-pin on specific pins so the Cape can communicate w/ the BBB. Once you have set up the config-pin utility, you may need to also figure out how to make the config-pin set up on boot or you will have to apply it each time in user space.