I posted this problem to the coreutils mailing list and got a response. The du from the current 6.9 version of coreutils is working nicely, so it doesn't seem to be a kernel problem.
http://www.gnu.org/software/coreutils/ (Note: coreutils 6.9 won't compile directly, due to a more recent change in glibc. Either use the current 6.9.90, or replace all occurences of "futimens" by "gl_futimens" (src/touch.c src/copy.c lib/utimens.c lib/utimens.h)) -- du reports existing files as missing https://bugs.launchpad.net/bugs/53388 You received this bug notification because you are a member of Ubuntu Bugs, which is the bug contact for Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs