It's not likely anything to do with the format of the drive, rather the host controller chipset in the drive is incompatible with older CDJs.
Pioneer DJ does not guarantee 100% compatibility with any USB drive. Functionality of one drive does not guarantee functionality of another identical make / model drive. Manufacturers are known to change the memory controller chip per availability or cost, and as a result, there is always a chance that a drive may not be compatible with the player host chipset. Recommendations or the results of another user may not be the same for you and your drive.