Thanks for your advice it is now working, this is what I needed to do.
I tried the SwissKnife tool mentioned by Th3_uN1Qu3 and well it didn't seem to work to well it all, when trying to format to fat it completely wiped the partition and left the disk in raw format.
So I went into system administration tools in windows and reformatted the drive from raw to fat16
Now here is where the brainwave struck, The rockusb player has a record voice function so I thought I would get the player to make the first write to the disk with this, rather than moving files over in windows straight after the format.
So I unplugged the player, recored a couple seconds of voice and it happily wrote the wav file to the disk. Now I plugged it back in to the PC and could see the voice directory on the disk, now I copied some files over, unplugged switched player back on held breath and yay the files appeared.
So in short it seems that if you have this problem, format the drive (fat 16), unplug, record voice, plug in, move files, all good.
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