I don't have experience with that particular unit but I do recall similar problems with my alpine units usb interface.

In my case the head unit would only recognize flash drives in fat32 format. Unfortunately this format limits you to 32gb if I recall correctly.

I was able to install a 300gb hardrive in my center console by partitioning in 32gb sections.

Folder structure on the alpine unit didn;t matter as you can browse the subfolders.

My suggestion is search online for a manual for the headunit and check the usb format compatibility or if you have some spare time try reformitting your drive temporarily (I seem to recall difficulties doing this with newer versions of windows, and booted up the old win2000 os lol)