Solution
By using the DAQmx Digital Write function, the hardware USB 6XXX devices is using software timing for its digital output. Software-timed digital output is dependent on the timing of the operating system and code. If using a non-real-time operating system like Windows, there will be larger jitter and the timing will also be affected by other processes happening on the computer. For more information regarding software versus hardware timed, please refer to
Timing, Hardware Versus Software.
The USB 6001, 6002 and 6003 have analog outputs that can be software timed or hardware timed. Hardware timing allows for less time between sample generation and timing can be deterministic. The fastest rate a square waveform can be generated is 5kHz, which may prove better than the digital waveform for some instances.