Is the one that doesn't work possibly formatted exFAT? Drives need to be FAT32 or HFS+ for rekordbox / devices to recognize them. They can also only have 1 partition, no security partitions or other features enabled.
It's always possible the drive simply isn't compatible with the device you're connecting it to due to a conflict between the USB memory manager chip and the player USB host chip. If you can tell us the make / model of the USB drive that is not working, as well as which unit it's not working with, that may help diagnose this further.