Same thing here:

Linux inspiron 3.2.0-25-generic #40-Ubuntu SMP Wed May 23 20:30:51 UTC
2012 x86_64 x86_64 x86_64 GNU/Linux

jon@inspiron:~$ dpkg -l | egrep ecrypt
ii  ecryptfs-utils                         96-0ubuntu3                          
    ecryptfs cryptographic filesystem (utilities)
ii  libecryptfs0                           96-0ubuntu3                          
    ecryptfs cryptographic filesystem (library)

jon@inspiron:~$ shred .gconf/apps/gnome-terminal/profiles/Default%gconf.xml.new 
                                                                                
                                                    
shred: .gconf/apps/gnome-terminal/profiles/Default/%gconf.xml.new: fallo al 
abrir para escritura: Error de entrada/salida

I did run out of space a couple of weeks ago. I tracked down the files
by their inode number and found at least 20 files. I had to delete the
files manually. There was real damage :(

I'm wondering if I should step out encrypted partitions

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https://bugs.launchpad.net/bugs/957843

Title:
  files in eCryptFS Private directory get corrupted

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