LEDs do not flicker natively so we know the problem lie in the circuit driving the LED. First step in any troubleshooting is to closely inspect your wiring. Double check every wire routing, connection, etc. It wouldn't be the first time an errant strand of a wire touching something has caused a problem. Process of elimination may also help. Disconnect the motor leads. LED work correctly? Bypass the plug. LED work correctly? Take the LM out and connect it directly to track power. LED work correctly? And so on.
Can you accurately describe to us in words the flicker effect i.e. evenly spaced pulses, random erratic pulses, LED gets dimmer as it pulses, etc.? Or better yet, post a video. Does the LED work properly when in full brightness mode? Does the HC report any warnings while LED is in dim mode?