Comment 10 for bug 416981

I noticed this weird behavior a few days ago, I also use an encrypted home (created my the ubuntu installer), so it might be the cause of the issue.
My details:
Jaunty 9.04 amd64
$ uname -a
Linux nexon 2.6.30-9-generic #10-Ubuntu SMP Wed Jun 10 12:45:25 UTC 2009 x86_64 GNU/Linux (have to run this because of the intel vga...)
$ du --version
du (GNU coreutils) 6.10 (...)
# aptitude show coreutils | grep Version
Version: 6.10-6ubuntu1

tests (using the same directory):
$ du -sh
92K .
$ du -shL
92K .
$ du -sh --apparent-size
131M . (this is correct!)

after I copied this directory to the root ext3 fs (which is not encrypted):
$ du -sh
108M . (not correct)
du -sh --apparent-size
131M . (this is correct again)