Not enough current draw through MOSFET
Here's a low side switch with a 250 mA load current and a 2.5A active current limiter .  If you disable the current limiter the supply current spikes up to 17A in this simulation.

Theory

Unknown Pi load capacitance causes low side switched supply to shut down from over current causing it to cycle on-off.

Soft start solution



Here is what I think the problem is.
  (Ignore transistor which is bypassed now and current spike is 17A)