Official comment
@Nic > Are you clicking the eject button within rekordbox or the OS? The R1 is a unique product in that the export requires the database to be written last, at the time of disk eject, rather than after the transfer has completed.
The other thing you need to do is ensure that you've got the database type set to XDJ-R1 in the rekordbox preferences, under the CDJ & Device page, on the Device tab. Select XDJ-R1 under the "Create library exclusively for:" option.