Unable to view *certain* folders on a USB disk shared by Airport Extreme

I have a 1 TB FAT32 formatted USB drive shared over an Airport Extreme (firmware 7.4.2).
A few days ago I was reorganising media files on the hard drive. I created a subfolder in a folder called 'Movies' and copied a couple of VOB files into the subfolder. Suddenly, the entire contents of the 'Movies' folder vanished. I unmounted and re-mounted the shared disk on the Mac (browsing to the base station in finder and clicking eject). I am able to see all other top level folders and other files on the shared drive, but the 'Movies' folder is empty. The Airport logs indicated a problem with the volume, so I disconnected the drive from the airport, plugged it into the mac and ran disk utility to verify the disk. No errors were reported.
Here is where it gets interesting.
1) When I plug the USB drive into my Macbook Pro, I am able to mount the drive and browse all the directories, including the Movies folder - all my files are still there.
2) If I plug the disk back into the airport and mount it on the mac, the 'Movies' folder appears empty.
3) The hard disk usage reported (both in the airport utility and in finder) is consistent with the 'Movies' folder still being there, however the Movies folder shows up at Zero bytes in 'Get Info'
4) If I open a terminal window and cd to the mounted hard disk, 'ls -al' reports no files. However, I can 'cd' to a sub-directory of the Movies folder that I know exists, and 'ls' shows all the files in the sub folder!
I can even copy files in the 'Movies' folder to another location if I know then name - but 'ls' cannot see it, and neither can 'du'
5) I attached the drive to a Windows machine and ran chkdsk and even did a surface scan - no problems reported.
I'm stumped. Has anyone seen this wierd behaviour before? The disk is fine when mounted directly on a mac or windows machine - but when mounted and shared via the airport, the Movies folder is not visible, though it is definitely there!
Help appreciated!

Hello nikkjazz. Welcome to the Apple Discussions!
The 802.11n AirPort Extreme Base Station (AEBSn) supports USB storage devices that use a block size of 512 bytes ... and is true whether the device is formatted for HFS+, FAT16 or FAT32. If yours is not, then it may explain why you can see the folders when the drive is directly attached to the Mac, but not so when connected to the AEBSn.

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