Hi Bobbie,
The counter's on the 6602 make use of a 80MHz oscillator. The frequency on the output should not be off by more than +/- 1 clock cycle. At 80MHz, this is a very small error (less than 6 ns). So I don't believe the error is with the generation. How are you measuring the period?
One approach would be to use the example program measuring frequency using 2 counters. Using 2 counters greatly increases the accuracy of the measurement. Simply measuring the period using 1 counter will not be as accurate. The shipping example "Measure Frequency (NI-TIO).vi" is a good example to try in terms of getting accurate measurments.
Hope that helps. Have a good day.
Ron