I managed to arrange a swap of the defective unit for a new unit with my supplier today. I had to wait a while because they had to get a new supply of units from their distributor.
I hooked up the new unit, registered it with Arturia, played around for a short while and then started Minifreak V again. And yes it was running in stand alone mode, before you ask.
It again told me that I needed to update the firmware from v1.0.0 to v1.1.0 and I let it do the upgrade. After the application told me that it was done and had rebooted the MiniFreak, I saw again the dreaded pulsating Assign page 1 LED still blinking, just like last time.
I think you can guess the rest, after a few more attempts with the bootloader mode it is now in a state that it doesn't want to enter that mode again. The difference with the first one is that on power on the animated Minifreak logo keeps spinning i.s.o the display staying blank.
There seems to be a fundamental issue with either the update process, the file used for updating or the flash memory used on the Minifreak.
I don't know which of these items is causing the problem, but the fact that I now have a second bricked Minifreak and that at least one other user has had the same issue happen to him, leads me to believe that this is a more widespread problem than just one single unit being faulty!