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The amber LED blinks when you get to some nonzero throttle because it ramps the PWM duty up to 100%, but is still receiving 0 amps of feedback current, which is bad. So, the PWM isn't making it all the way to the output of U7. I would theck the voltage at R11 (either side of the resistor) relative to the back of U1 (ground) when you give it throttle. It should climb from 0v to 5v. Then, if that's happening, the PWM from the microcontroller is working, and we can move to the voltage at the left side of R15 relative to the back of U1 (ground). If that is inverted (it should go DOWN as throttle goes UP, then check the bottom of R16 relative to PH1 or PH2 while you give it some throttle.
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