If you turn on hightlight execution when this happens, does it appear something is running, or a particular function is hung up?
Is what is being read at the analog input based on what is being sent out at the analog output? The two parts of code are running in parallel. I'm wondering if something takes too long in one part, the other part is done executing too soon.
I would convert the feedback node in teh analog read loop to a shift register. I think what you have is okay, but if I want to be certain that the shift register is re-initialized when the VI restarts, I'd turn it into a shift register and move the constant outside.
Are you sure about your conditions for incrementing the counter in the top loop. You have AND all array elements. Maybe all of those elements aren't staying above the threshold long enough and the read loop keeps running?
Make sure you use troubleshooting tools like probes to see what the data actually looks like and know if the code is executing.
