Here is what I “think” is going on. The Fan Control pin is pulled Low to turn the fan off. Thats done so the fan runs even with no software installed. It just runs continuously because the control pin is floating high.
On boot up, before the fan shim software starts running that pin is floating, so its effectively high. Fan is on.
Software loads and pulls that pin low, fan goes off. Until the temp hits the threshold to turn it on again.
Shut the Pi down and that pin goes back to floating High. fan turns on.
With the original eeprom code the +5V and 3.3V were turned off. The fan goes off as it doesn’t have any 5V. The Pi won’t boot up via GPIO 3 though.
With the new eeprom code the +5 and 3.3V stay on. The fan stays on as it now has 5V and the fan control pin is high. And the Pi will now boot up if your ground GPIO 3