I just gave it another go, this time using the casper file that Steve
sent me over the email. The problem is now fixed completely.  (not sure
what happened to my patch on casper file, it said it was done
successfully)

thank you so much, Steve.

It surprise me how few instances of this problem have been reported on
the internet. I suspect that a lot of people sees it as a bad sector
problem with their usb drive. I, for one, spent hours doing surface
scan, low level format, trying to solve this issue.

If it wasn't for Steve's post on bug 371477, I would never have found
this thread and solve this problem.

If this bug occurs in every ubuntu persistent install, then it may be a
good idea to give it a bit more attention? the pendrivelinux.com people
should make a note of it if the problem does indeed occur everytime.

-- 
casper-rw fs not cleanly unmounted on persistent live USB shutdown
https://bugs.launchpad.net/bugs/125702
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