You placed a Logic Converter not a Logic Analyzer. The converter works with circuits containing gates such as AND, NAND etc... it won't work in a circuit with flip-flops.
All left-pointing pins on the analyzer are inputs, you can use any pins to analyze your circuit. When you double-click on the instruments, click the "Set" button under the Clock area, set the clock rate to twice your highest frequency.
Download a counter datasheet from any manufacturer and you can see how they care a truth table.
Tien P.
National Instruments
