Hello;
The buffered period measurment should work in a way that at each event of an active edge at the gate input of the counter, the current value of the counter will be buffered in.
If you did the proper connections in between the pulses and the counter inputs, my suggestion is for you to double check if the incoming pulses are meeting the specifications of the counter, and also look for glitches in the signal.
Hope this helps.
Filipe A.
Applications Engineer
National Instruments