The Timezone under Linux as just a symbolic link to an appropriate timezone file in the /usr/share/zoneinfo. It may happen that your time within GUI applications is correct, however time on the command line is wrong. One of the possible reasons could be that your system's timezone is not set correctly. To set you correct time zone first investigate what file from /usr/share/zoneinfo would be appropriate for your timezone. For example if you are from Europe/Slovakia you would set your symlink as follows:

# ln -sf /usr/share/zoneinfo/Europe/Bratislava /etc/localtime

Now you can set correct time with ntpdate command:

# ntpdate

If you do not have an internet avaiable to set your time to NTP server you can also set your time from you hardware time ( assuming hardware time is correct )

# hwclock --hctosys

Confirm correct time with:

$ date