Recently for a client we had a very peculiar problem: a nightly script which checked if a person has done a certain action that day was always flagging everyone. We tested the script multiple times on our servers and it always worked fine. The query had something similar to this:
SELECT * FROM action_table WHERE DATE(action_table.time)=DATE(NOW())
Well after a while of trouble shooting we found out that the system clock on the clients server was skewed and in the wrong time zone. We synced the machines clock and update its time zone. Before it had been in UTC time and we switched it over to EST. What is interesting is that MySQL did not respect the new time zone of the clock, it was still reporting as if the system was set to UTC. We then did a soft restart(reload) on the MySQL service, but it still maintained that it was in a UTC timezone and not EST. It took a hard restart of the MySQL service to have it respect the EST timezone.
All in all, as far as we can tell you need to restart the MySQL service to have it respect a new timezone.