I think that the ideal solution for you would be to set up a retriggerable finite pulse train operation on one of your counters.
On your computer there are some examples in the
C:\Program Files\National Instruments\CVI71\samples\daq\Ctr directory, then you might want to take a look at
STCgenerateRepeatedTriggeredPulseThat should show you how to do a repeated triggered pulse. Now instead of doing a single pulse, you just need to generate a finite pulse train.
You can find an example of that here:
Generating a Finite Pulse TrainFinally there is this example:
Retriggerable Analog Input using CVI and E Series DAQ BoardsIt does what you are trying to do, but applies the retriggerable finite pulse train as the clock for an analog operation. You could just strip out the parts for analog input operations.