I am encountering a similar problem.  I'm running Ubuntu 8.10 off of a
pendrive (with persistent data enabled).  Here are the steps / symptoms
I'm seeing:

1) Set up the timezone, etc. and see the correct date/time reported on
the toolbar.  My timezone is "America/North_Dakota/Center".  I've used
"sudo dpkg-reconfigure tzdata" to set my timezone, and have confirmed
that "/etc/timezone" matches my setting.  Doing a 'diff -s
/etc/localtime /usr/share/zoneinfo/`cat /etc/timezone`' indicates no
difference (as expected).

2) Reboot.

3) The date/time on the panel bar now reads +0600 hours local time
(local time = 9PM CST, panel bar time = 3AM")  On the command-line
'date' similarly reads UTC instead of CST.

4) Go to System > Administration > Time And Date

5) "Time Zone" now is blank.  In step 1) above, I had set it to
America/North_Dakota/Center".  /etc/timezone is still correct.  However,
'diff -s /etc/localtime /usr/share/zoneinfo/`cat /etc/timezone`' now
indicates a difference - this is unexpected.  Doing a 'diff -s
/etc/localtime /usr/share/zoneinfo/UTC' shows an identical match.

I'm guessing that something at either power-down or boot-up is
forcefully updating /etc/localtime.  Might be simply a matter of
figuring out what and why.

-- 
timezone info is forgotten at reboot
https://bugs.launchpad.net/bugs/308983
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