Was your flash drive formatted under NTFS or FAT32, exFAT? I don't remember which one I had the problem with, but it seems I had an issue when formatting with NTFS, or was it exFAT. Reformatted with FAT32, reloaded the music and all is happy. There may be a flash drive data size limitation with Uconnect 4 which I forgot...64MB, 128MB??
Which Radio do you have 8.4, 12?
Uconnect 4 or Uconnect 5?
As far as folders, you may be able to access a folder's music through the Browse Button. It would play only from that folder...IF my memory i correct.
Uconnect 4C manual:
Browse
Press the Browse button on the touchscreen to display the browse window. The left side of the browse window displays a list of ways you can browse through the contents of the USB device. If supported by the device, you can browse by Folders, Artists, Playlists, Albums, Songs, etc. Press the desired button on the left side of the screen. The center of the browse window shows items and it’s sub-functions, which can be scrolled by pressing the Up and Down buttons to the right. The TUNE/SCROLL knob can also be used to scroll.