Another approach to consider:
Stream the data and the trigger line to disk as one complete capture lasting the full duration of the run then post process the captured data to remove the portions where the trigger line indicates bad data, this should remove any of the delays in stopping/ starting the recording, if you create the code to do the record then go straight in to the post process I don't think it will add too much time to the overall task, the 6024 board should be capable of far higher speed than 2KS/s on a couple of channels - Mike
