All of Yamaha's S series keyboards should have already been inspected at the factory where they were produced i.e. China. With all the apparent quality control issues Yamaha is experiencing with the S series a second inspection couldn't hurt at the Buena Park facility i.e. Yamaha U.S. in Buena Park, CA. where the keyboards are distributed from.

The USB media (thumb drive etc.) must be self powered, requiring no hub driver. I have found Lexar Jump Drive PRO thumb drives to work flawlessly with my past Motif XS7 and my current Roland Sonic Cell PRO. When formatting the thumb drive it is recommended to format the drive in "FAT" not FAT32. I'm not sure if the USB media for the S900 in question was formatted in FAT or not but I would think if the drive worked in the PSR3000 then it should have also worked in the S900. The quickest way to test the theory would have been to save the present files on the drive to a folder on your computer then reformat the thumb drive in FAT from the computer, add some files back onto the thumb drive making sure to keep every file added in the root directory and then try re-inserting the thumb drive into the S900 USB to Device port to see if it then recognizes the drive. If the new S900 on the way has the same problem with recognizing the USB media, then I would tend to think that the problem is not with the S900 but with the USB media.

Best,
Mike