I get the same problem on feisty:
emmy:/media/sda2$ du --max-depth=1
641440  ./i386
10880   ./valueadd
40768   ./dotnetfx
3008    ./book
224     ./sysinfo
3778080 ./windows
2097088 ./Documents and Settings
4787328 ./Program Files
du: `./System Volume Information': No such file or directory
du: `./found.000': No such file or directory
du: `./Recycled': No such file or directory
.
.

emmy:~$ uname -a
Linux emmy 2.6.20-15-generic #2 SMP Sun Apr 15 07:36:31 UTC 2007 i686 GNU/Linux

emmy:~$ mount |grep sda2
/dev/sda2 on /media/sda2 type vfat (rw,utf8,umask=007,gid=46)

I don't think I've ever used an ext2fs driver in windows on this
machine.  The partition that displays these problems is vfat anyway.

-- 
du reports existing files as missing
https://bugs.launchpad.net/bugs/53388
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