I'm also having this problem on Jaunty:

$ mount | grep home
/dev/mapper/MAIN_VG-HOME_LV_crypt on /home type ext3 (rw)
/home/user/.Private on /home/user type ecryptfs 
(ecryptfs_sig=ace5d3dc7966c556,ecryptfs_fnek_sig=c0bd3cca6d89c7fd,ecryptfs_cipher=aes,ecryptfs_key_bytes=16)
gvfs-fuse-daemon on /home/user/.gvfs type fuse.gvfs-fuse-daemon 
(rw,nosuid,nodev,user=user)
$ dd if=/dev/zero of=test123 count=234333
234333+0 records in
234333+0 records out
119978496 bytes (120 MB) copied, 10.1632 s, 11.8 MB/s
$ du -sh test123
0       test123

Note, it happens with newly created files or directories. It doesn't
matter what they're created by...I noticed this when I was creating a
very large Lucene index yet du was telling me the directory was empty.

In my case, the index directory actually did show size after a
reboot...but it took the reboot to make it happen.

Please, please, if there's any way, issue a patch for this. It's very
frustrating, and I really don't have the option of redoing my home
directory at the moment.

Thanks!

-- 
du reports newly created files on ecryptfs as empty
https://bugs.launchpad.net/bugs/390833
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