I took a look at your VI and I am not sure what the problem is, however the VI you attached is not a complete working VI, so I may be looking at the wrong code.
Anyways you are collecting 1000 points at 1000pts/sec. Therefore the AI Aquire Waveform VI will take 1 second, and then after that you will then start to save data and do your analysis and then the anaolog output. So I would expect that your loop rate would be higher than 1 second, although I would be surprised if it is was exactly 2 seconds.
