Lots of different reasons why it's not working. Could be the clock. Could be the solenoid valve. Could be the wires.

You know that zone 1 and 2 work. Hook zone 1 or 2 up to zone 3 and see if it works. If it does then you know that the clock is fine. If it doesn't then the clock is broke and you'll probably have to return it. You could also hook zone 3 up to zone 1 or 2 but if it doesn't work it doesn't automatically mean that the clock is broke since the problem could still be in the wiring or valve.

If zone 1 or 2 works fine on the 3rd zone then you could have a problem with the solenoid valve or a short/cut line. You can try turning on zone 3 and using a voltmeter to see if you are getting 24volts at the valve. If not then you probably have a problem with the wires. If so then it's possible the solenoid is bad. You can pull the solenoid and hook it directly up to your clock to see if it works that way. Solenoids are normally replaceable.

Lots of things that could be wrong. Could be a broke water line heading out to that zone also although you'd probably notice a soaked spot in the yard. Could be a clogged valve.