I have some trouble today 31.10.2011, my Jira 4.1 switches to winter time, but does not, because we have patched our Java (in 2011 in Russia stops time switching). Now my system time in System info is right, but time stamp is one hour before.
Resolution: repace file with incorrect timezone under jar \atlassian-jira\WEB-INF\lib\joda-time-1.6.jar. Correct timezone file can be founded in current version of joda-time.jar, available on official site http://joda-time.sourceforge.net/.
Just replace timezone file and restart JIRA.
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