Hello;
You probably didn't specify the counter source pin to get the input from the connector, and the way the counter is configured, it's probably reading the pulses from the internal Timebase.
If you are using Labview, there is a vi named Source.VI (can be found in any one of the counter examples) that allows you to configure the source input for the counter. If you are using NI-DAQ function calls, double check the shipping examples for your programming language to get familiar on how to change the counter source input.
Hope this helps.
Filipe A.
Applications Engineer
National Instruments