@chrishamm interesting; perhaps there might be some delay issue?
The power supply goes as follow:
24V PSU ------- Duet 3
\______________ 5V DC/DC PSU ________ Rpi 3B+
With the 5V Rpi jumper removed as follows:
5V enable ON,
Duet --> SBC OFF
SBC --> Duet OFF
Perhaps the rpi power up a fraction of a second too late as powers through the additional 5V DC/DC converter?
That might also explain why it would start up fine after a repower; perhaps thanks to some residual juice in that 5V PSU?
Could disabling the 5V Enable jumper and jump SBC --> Duet be worth trying?