Solution
I/O signal rate is the maximum frequency of the input signal to be measured and for NI 9361, it is specified at 1 MHz. The reason it is specified at 1 MHz is because when the device measures beyond 1 MHz, the front-end circuitry will cause degradation to the signal rise and fall time that might impact the accuracy of certain measurements such as duty-cycle. In reality, since the counter timebase is 100 MHz, it can still measure I/O signal rate beyond 1 MHz though the measurements might no longer within the device specification.
Therefore, when using NI 9361, it is highly advised to set the maximum I/O signal rate to 1 MHz as per stated in the specification.