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After putting up with it for a couple of day, i finally had enough...
Went to google for a solution. Came across this blog that recommended deleting some files in the profile's update directory. However, i am worried that that might caused some other problem. Apparently, the issue caused is because when the application is not running in administrator mode in Vista computer, it do not have privileges to do lots of things.
So the simple solution is to close Thunderbird and use "Run as administrator" to start it up.
After that, it updates successfully and the irritating message is gone!