Hi guys,
I've been having the exact same issues since I got the XDJ in February. I've asked on here a few times but no help that solved it. I figured out a work around but it's time consuming. It seems to me it's either an XDJ-RX fault or a fault in the transfer from Rekordbox to the USB. Have a look at my thread I've just started and the link within it for my work around:
https://forums.pioneerdj.com/hc/en-us/community/posts/207780103-Rekordbox-transfer-to-USB-problem-