1. what type of filesystem is this?

Information from 'mount -v':
...
/dev/sda12 on /home type ext3 (rw,relatime)
...
/home/username/.Private on /home/username type ecryptfs 
(ecryptfs_sig=60cc62a1039711h8,ecryptfs_fnek_sig=3257a12b81aff999,ecryptfs_cipher=aes,ecryptfs_key_bytes=16)

So, it's an encrypted home directory on an ext3 partition.

It might be ecryptfs related maybe?

2. is it local or remote?

local

3. does it happen on other directories/FSs?

Yes, most certainly! I pulled three projects from a Perforce server, all
seem to report the wrong size with 'du -hsL'. In some cases, the
difference is factor 2!

4. can you copy it to another place, and test again?

I guess you assume to copy it to a non-ecryptfs filesystem. Sure thing.
Result:

Original folder now shows 59M copied to /home (local ext3), Nautilus
shows 54M on ecryptfs and on ext3. So it's closer, but not identical.

-- 
coreutils: du(1) doesn't summarize correctly
https://bugs.launchpad.net/bugs/416981
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