It's the 64GB one:
Something was definitely strange:
after posting I noticed that changes in the settings were lost, additionally installed packages got vanished and uninstalled packages reappeared after a reboot. Might have been this but to be save I flashed an ext4 image (instead of squashfs this time) on a spare SD card which I'm using right now.
I don't know how to check the 64GB's health though. From what I could google it seems SD cards don't make bad sectors transparent to OSs...