I have had problems with the clock on one of my Ubuntu computers. The NTP (Network Time Protocol) service is supposed to take care of synchronizing the clock, and the GUI has settings for this. However, and but it did not work (Ubuntu 11.10), as the clock was constantly delayed.
The fix was simple, (re)installing the ntp package made sure that some of the missing dependencies was installed. I am pretty sure this has happened to me before, so it could be a useful tips to others. If your clock runs late, try the following (one may of course use Synaptic as well):
sudo apt-get install ntp