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You're correct, they just use the system's current time. The typical way I've seen to synchronize time across computers is to use Chrony. With Ubuntu, you should be able to just run apt-get install chrony.

Here are some resources I've found on a quick search:

http://answers.ros.org/question/2140/chrony-configuration-and-limitations

http://pr2support.willowgarage.com/wiki/PR2%20Manual/Chapter13#Clock_Synchronization

The important information is that your ROS system computers are tightly coupled in time, but loosely tied to the outside world's time.