How do you stop the program? I see an architecture problem as you have to hit 3 different stop buttons. Why do you have so many while loops nested in while loops? Many of those inner while loops will start executing again after you hit their stop buttons. Because the outer loops such as stop 3, is read as false before the inner loops start running. You can and click all the stop buttons, but since the outer stop has already been read, it won't read it as true until its next iteration, which means the inner loop will start again.
I don't know what your extra while loops are needed for, The outer while loop in the lower error case is particularly pointless as the only other code inside of it is another wait function. And the outermost while loop of the whole VI pretty much just wraps the two parallel loops.
