I created a bootable USB stick for Ubuntu 12.10 using Unetbootin and set the persistent file size to 3072mb. I am able to boot into Ubuntu 12.10 just fine. However, any changes I make are lost on reboot.
Follow the tutorial HERE if you were successful building and booting the thumbdrive then I would check as to what format you used.
For a persistence to exist the thumbdrive needs to be formatted in FAT32. They other thing is I have never set the persistence to more than 1/3rd of the total capacity of the drive. This has been the rule-of-thumb or (thumbdrive) for me.