To easily measure the frequency of a pulse waveform, you should try using a Counter on your DAQ card instead of an analog input.
The counter will give a much more accurate frequency reading and even have the ability to filter noise. You'll still have to use the analog inputs if you want to display the waveform on the front panel, but I think you'll have much better luck getting the frequency using a counter.
Check out the Counter examples that ship with LabVIEW to get started.
Ed

Ed Dickens - Certified LabVIEW Architect
Lockheed Martin Space
Using the Abort button to stop your VI is like using a tree to stop your car. It works, but there may be consequences.