Hi Rob,
I believe it has to do with your source and gate choices. The NI-TIO counters, which are the counters on the 6601 card, count each time they receive a rising edge on the source input (or falling depending on configuration). There is one exception. If the gate signal is low, the source signals are ignored and the counter doesn't count. If the gate signal is high, the counter will count all source signals. This uses an active high gate (could be configured active low as well).
What this has to do with you is if your source signal has a low rate, it is more likely that your faster gate signal is causing the counter to ignore the source and not count. Typically, the faster of the two signals is used as the source.
Theoreticall
y, it is possible that your source signal is never counted if it happens to produce a rising edge when the gate is low. That is why the source signal should be at least twice as fast as the gate.
Anyway, I'm not sure if I misinterpreted your post or not. Let me know if I did. Have a good day.
Ron