On your page http://docs.kali.org/installation/kali-linux-encrypted-disk-install , you wrote (in both(!) sections, unencrypted and encyrpted persistence):

"… we create a 5 GB persistent partition and create a persistence.conf file on it.

size=5gb
read bytes _ < <(du -bcm kali-linux-1.0.8-amd64.iso |tail -1); echo $bytes
parted /dev/sdb mkpart primary $bytes $size

The problem is "$size".

AFAIK, "parted" requires two parameters " … START END", but your current text implies that it treats the parameters as "… START LENGTH" (i.e. $size).

When you verbatim run the example, you will end up with a persistence of size (5gb-length(kali)) because Kali 1.0.9 is 0000002:0000002,9 GB which resulted in 0000002:0000002,8 GB persistence only instead of 5 GB.

I suggest that you correct this part (in both sections).