I tried the software reboot solution with a small program that simulates the "A+A+CTRL" key combination (it calls the Exec Library reboot command) and it does not work! I HAVE to press the keys!!!
The difference is that Ctrl-A-A does a real hardware reset, just like if you pressed the reset button on the tower case. The program only does a software reset. It is not able to reset the entire hardware.
HELP!!!
It seems like your hardware is not able to deal with software resets, so you should avoid them. Try to rename the file "AmigaOS ROM Update" in the Devs directory. Then OS 3.9 will no longer soft-reset on the first boot.