I created a new SD card using the "old method". After booting I got a "No File" message and no menu. I could ftp and ssh into MISter so I decided to run the update script to see what would happen. As soon as I started the script I realized that I completely forgot to create a MISTer.ini.
I let the script finished and planned to fix the MISTer.ini after that. As the update contained a new Main it rebooted MISTer and surprise: no more No File message and F12 brings the menu up while I still had no MISTer.ini (which I promptly fixed).
Was the original message indirectly caused by the missing MISTer.ini?