I have noticed this also and it is very annoying. After updating the retropie setup script the randomizer is disabled and needs to be enabled after each update...

I still have a question related to this topic.

My workaround works, but it requires a reboot of my RPi which is not very convenient - does anybody know a way of disabling a CPU core online? On non-ARM CPUs it is possible by echo'ing "0" to /sys/devices/system/cpu/cpuX/online, but here it won't work.

Thanks.