I have been experiencing this problem for many times and it happens when I'm using my external HDD formated to FAT32 with many folders and subfolders, and with mp3 beeing not analized by Rekordbox. I have so many folders with subfolders dividing music by date and genres so I will never bother spending my time re runing it through rekordbox.
When I'm starting deejaying everything works fine - I can see files in my folders and subfolders, but after a while everything stops working properly. Some folders are indicated as EMPTY and the only solution to this is to re-start AERO. It works fine for a while but brakes again and again. I started carrying with me CDs so that I can use external CD player via a different mixer when I'm restarting AERO.
I have just upgraded from 1.02 to 1.06 firmware, so the most up to date firmware and it didn't help. For me it is a definite fault of the firmware and might be something to do with a use of the internal memory of the AERO which after remembering reading data is full and cannot process any more of it.
Pioneer, please sort it out! Running all my music through Rekordbox is not an option.
Another related issue is Rekordbox on my iPhone. When the song is not analized and I load the song into AERO it keeps warning each time that it was not analized. Why there is no option of turning it off? It is annoying.