After some experiments, I found that after some time being powered on, the peripheral supply voltage becomes unstable. As far as I can tell, the voltage is being regulated by a current limiter that drops the voltage every time the LEDs blink. Once it is in this current-limiting mode, the peripheral supply does not reset until the pixhawk is rebooted.
The strange thing is that this problem only appears in recent batches, and we have made no hardware changes. We are drawing less than 400mA on the peripheral supply, so it shouldn’t overdraw it. Also, the Pixhawk logs do not show that an overcurrent state was detected.
I am not sure if this is related to this issue, but it sounds similar. The difference is that we are experiencing this with Cube Black, not Blue (have not tested Blue).
(It may be appropriate to move/rename this thread out of the HERE forum)