Comment 4 for bug 372014

The same:

$ dmesg | tail
[32955.246231] Valid eCryptfs headers not found in file header region or xattr region
[32955.246248] Either the lower file is not in a valid eCryptfs format, or the key could not be retrieved. Plaintext passthrough mode is not enabled; returning -EIO
[33019.249402] Valid eCryptfs headers not found in file header region or xattr region
[33019.249418] Either the lower file is not in a valid eCryptfs format, or the key could not be retrieved. Plaintext passthrough mode is not enabled; returning -EIO
[33573.256403] Valid eCryptfs headers not found in file header region or xattr region
[33573.256420] Either the lower file is not in a valid eCryptfs format, or the key could not be retrieved. Plaintext passthrough mode is not enabled; returning -EIO
[33651.229472] Valid eCryptfs headers not found in file header region or xattr region
[33651.229484] Either the lower file is not in a valid eCryptfs format, or the key could not be retrieved. Plaintext passthrough mode is not enabled; returning -EIO
[33713.245151] Valid eCryptfs headers not found in file header region or xattr region
[33713.245163] Either the lower file is not in a valid eCryptfs format, or the key could not be retrieved. Plaintext passthrough mode is not enabled; returning -EIO

As far as zero byte files goes, I found the following:

$ mount | grep crypt
/home/tobuntu/.Private on /home/toobuntu type ecryptfs (ecryptfs_sig=[sanitized],ecryptfs_fnek_sig=[sanitized],ecryptfs_cipher=aes,ecryptfs_key_bytes=16)

$ find /home/toobuntu/ -xdev -size 0c -exec ls '{}' \; | wc -l
233

Hmm, here are some examples:
$ ls -lAhS | tail -n 5
-rw-r----- 1 toobuntu toobuntu 0 Jun 24 09:12 .gksu.lock
dr-x------ 3 toobuntu toobuntu 0 Jun 24 09:11 .gvfs
-rw-r--r-x 1 toobuntu toobuntu 0 Mar 1 13:56 .nofinger
-rw-r--r-- 1 toobuntu toobuntu 0 Mar 30 07:06 .screenrc
-rw-r--r-- 1 toobuntu toobuntu 0 Mar 1 00:35 .sudo_as_admin_successful