Yes, cities with the same time zone are hardlinked together. THey are
being made available under different names, so that they are easier to
find for an user. Or are you saying that the duplicates actually have
different time zones?
If they are indeed the same, then this is just a g-s-t bug, since with
the tzdata package itself, as well as glibc, gnome-panel, etc. it works
fine.
** Changed in: tzdata (Ubuntu)
Status: New => Incomplete
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time-admin shows different time zone when it is restarted
https://bugs.launchpad.net/bugs/43644
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