I repro the "no persistence" on several separate ubuntu machines. I
don't recall the attempts to write making the stick unbootable though.

Was using a 4GB corsair, freshly formatted fat32. ubuntu 8.10 and 9.04
AMD64. I maxed out the persistence file size for my stick (about 3.1
GB). usb-creator proceeded to write the iso to the disk but at the end a
small window with a red warning circle with a white horizontal line
appeared. There was no text message. I closed that out & rebooted. It
booted into the live system properly. I created a small text file on the
desktop and one in /   . neither one persisted through a subsequent
clean reboot.

As a test I later manually created a casper-rw file in the root of my
usb stick (there was not one present) and persistence started working. I
see the casper packages are not a dependency of the usb-creator package.
Lupine: do you have them installed? I do not.

there's a thread over at ubuntu forums where several people report
problems w/ persistence:
http://ubuntuforums.org/showthread.php?t=1077904

-- 
No persistence with USB Creator in Ubuntu 8.10
https://bugs.launchpad.net/bugs/302485
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