One thing to be careful of is that you have a very clean squarewave. In my experience the counter input is very sensitive to over- or under-shoot, ringing skewed edges and the like.
Go into measurement and automation and select test panel for the card you're trying to measure the clock with. Go to the Counter I/O tab.
For Counter Mode select "Simple Event Counting" and from the Event Source pop-up select the pin you have the clock connected to. Press the Start button.
You should see the Counter Value go up each time a pulse happens. If it doesn't there's either something wrong with the signal--or your card.
If this works there is something else wrong with either the example code or your setup. I have also found out the hard way th
at there is NO buffering on the digital inputs and is is very easy to fry counters...
Hope this helps...
Mike...
Let me know what you find.