alegrecd,
I'm afraid I don't know the syntax for doing this from C with explicit DAQmx calls. But I think you need to look into turning ON the property called "duplicate count prevention." The name isn't the most descriptive of the actual behavior.
Normally the property is OFF. In such case, the counter expects the Source signal (which increments the internal count register) to be faster than the Gate (or "sampling clock") signal. If no Source edges are seen between successive Gate edges, the count value is NOT put into the data acq buffer.
If you turn the property ON, then the count values WILL be written to the buffer, even if no source edges have occurred between successive Gate edges.
-Kevin P.
CAUTION! New LabVIEW adopters -- it's too late for me, but you *can* save yourself. The new subscription policy for LabVIEW puts NI's hand in your wallet for the rest of your working life. Are you sure you're *that* dedicated to LabVIEW? (Summary of my reasons in this post, part of a voluminous thread of mostly complaints starting here).