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Counting with cFP-CTR 502

I have a number of tasks where I count events and frequencies with the cFP-CTR 502.  Turbine flowmeters and optical RPM sensors are the instruments I use most often.  I am a new programmer learning on my own.  I have been successful counting TTL pulses but would like to get a good period reading of the TTL.  I have read and seen the sample code that uses the internal clocks for this.
In experimenting with the internal counters (32Khz and 1 Khz) I notice that I read both counters 4 - 6% lower than their stated frequency.
Is that typical error?  Does anyone have any tips on achieveing this with a high degree of confidence?  I have looked at the one sample FP period measure VI but have had little luck making that work for me.  Any advice would be appreciated. 
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In reality, it is possible to see such errors. In the picture below, a clock signal (source) is being used to measure the period of the gate signal. 
If any of the rising edges of the source line up with the rising edges of the gate, then it is possible that the count will be slightly inaccurate and be a source of error for the result. 

The magnitude of this error would depend on the frequency of your signal.  What is it?
Also this possible max error will vary based on your source signal.

Period Measurement with a Counter

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