This post mentions the same behavior:
Pins 29, 31, 33, and 37 light up, but every 1.3 seconds or so, the brightness dips twice in short succession, in a rhythmic fashion. Apparently, these pins are 3V by default, and the working pin is 3.3V by default, so I’m thinking that the 3V regulator on this board is unstable for some reason, or that something is pulling the entire bus low, I’d like to set all the pins to use 3.3V, but I can’t find any documentation about how to do that.
I have also separately configured another pin as PWM, set it at a 100ns period and 50% duty cycle to match the waveform of the SPI clock and it exhibits similar behavior. This seems to indicate that the regulator for the 3.0V power domain(s) can’t keep up with the current demanded of it, even with only the on board devices (WiFi, SD card, etc.) connected.
Can you please confirm whether that’s the case and whether the issue is the HW design of the regulator itself, or some sort of configuration issue? If it is a HW design issue, that’d be good to know, so as not to spend any more time looking into this.