It is because all the inputs are 0 (which 0 < 3) on startup.
So you can do something like
a) if in11 is 5v, then variable "ok to shutdown" = 1, else "ok to shutdown" = 0. Delta timer that to 1000 or so.
b) if in11 is 0v AND "ok to shutdown" = 1, then send STOP. Delta that to be at least 1/2 of the above, so lets say 200.
The delta is the minimum time after the event has fired that another event will be fired for the same thing. So it will take another 1s for the first one to be fired, and another 200ms for the second one to be fired after being fired.