some USB files not showing on CDJ...help

So I had a bit of a nightmare playing at a club last week. I moved my tracks onto my USB stick (FAT32) and put them into different folders in case i needed to take the set in different directions. When i got to the club and put the usb into the cdj the main folder i wanted to start with that had all my new tracks was showing but the tracks in the folder werent. Same thing happened to two of the other folders i had set up on the USB, but the remaining 3 folders where totally fine. I get all my music from the same places bpmsupreme & beatport and i copied the mp3 files over the same way for all folders. Has anyone had this happen to them and if so do they know what causes it and how to fix it.

Maybe should mention too, I prepare my tracks with hot cues at home on rekordbox and export using the sync in export function, i exported all folders at the same time too. When i put the usb into my computer when i got home the tracks where showing and rekordbox was reading them fine too