As Windows behaves non-deterministically you will always see a non-deterministic delay (jitter) in your application. The only way to eliminate this jitter is hardware synchronization. In fact for high accuracy a trigger signal is not enough but you will need at least a board clock synchronization, too, to avoid drifting during the measurement.
By the way: Almost all
NI digitizers and
multifunction boards provide hardware synchronization, starting from simple
RTSI-bus synchronization (accuracy: several nanoseconds) and ending with high end
T-Clock technology (accuracy: several picoseconds).
Best regards,
Jochen Klier
National Instruments Germany