The root of the problem is the following, there is a difference between the array of shape (n, ) and (n, 1) in NumPy. So you need to reshape WeightsFinal when reloading the text,
WeightsFinal=loadtxt('WeightsFinal.txt').reshape(LayerSize, 1)
Now y_out.shape=(3600,1) before it was y_out.shape = (3600, )
This resolves the issue!