Edit: Read on another forum that /boot files get deleted after updating on some SD cards.
Temporary solution:
* update with pacman -Syu --ignore raspberrypi-firmware (tested and didn't break anything for me).
Disadvantage of this method is that your firmware will be out of date. I still have to use the .elf files to configure my GPU memory for example.
Edit: oh and as for the new rootfs: I doubt changing to ext3 will fix my problem, maybe for Arifmeticus it will work.