Hello;
Firts thing to double chekck is if you are doing buffered acquisition. If does, you need to make sure that your sample rate is set fast enough so teh acquisition task would take the 2000 samples you need, in between each trigger signal.
Your overall application is a retriggerable analog input task. I'm attaching a CVI example code of that type of task. You can refer to that example as a start point for your solution.
Hope this helps.
Filipe