Apologies for not mentioning that I use a SSD HD, not SD card.
The SSD HD is connected to a powered USB HUB (along with the RPi), in order to make sure it is always powered when the RPi restarts (I came to the conclusion that this was the reason for the issues I had rebooting my RPi).
Also, when I shutdown / reboot my RPi (through SSH or cron) should I first stop the openhab2 (or any other) service?