I have this exact same problem. I have two PNY 128GB USB drives (one is USB 2.0, the other is USB 3.0). Both are identical formats (FAT32). Both have folders and sub-folders (Music>Artist Name;Video>Artist Name). If I leave these drives in when I start the car, the radio will never fully boot. However, if I remove the drive, then plug the USB sticks in AFTER the car has started and the radio boots, they read perfectly and there's no issue until I turn the car off again.
Does anyone have any feedback/info on this? It's VERY annoying...
Thanks in advance!