If you start and stop the pulse by software under Windows you will never be able to determine the length of the pulse exactly due to non deterministic operating system latencies.
Things will improve if you run the pulse generation in an onboard on the 7344 as there is a deterministic real-time operating system running on it.
If you need to start the pulse at a specified position the most accurate method would be using the breakpoint functionality of the board to trigger an external counter device like the
PCI-6601 to generate a pulse with an adjustable length. The PCI-7344 and the PCI-6601 can be connected internally with a simple ribbon cable to share synchronization signals via the RTSI bus
without the need of external signal connections.
Best regards,
Jochen Klier
National Instruments Germany