Where in the manual do you see the Gate is configured as an output? It is actually configured as an input only. For the Measure Frequency VI, if you are using counter 0, connect the OUT of counter 1 to the GATE of counter 0 and the signal you are measuring to the SOURCE of counter 0.
What this is doing is, counter 1 is generating a pulse with a known width, 2 seconds for example. Counter 0 is simply counting pulses from the unknown signal for the duration of those 2 seconds.
Brian