Actually, I solved the issue. I’ll just leave it here instead of opening a new (and solved) issue.
It seems this output occurs when the boot partition (or another) gets corrupted. I use a standard image that I flash to Jetson boards to clone our application. Cloning the image to the board again did not solve the problem.
What I did to solve it was to reflash the board through the Nvidia SDK Manager. My guess is that it flashed all of the partitions fresh, thus eliminating the problem. From there I could flash my own image and everything works.