I'm guessing you're using the Extend X/Y Size to Area feature? If so this problem occurs because the optimum size of the array is calculated based on the size and shape of the spline, so as you change the spline the array size also changes. The best workaround therefore is to turn off Extend X/Y Size and instead manually set the size of the array using either the X/Y Size spinners or two splines. By separating the Clipping function and the size in this way you will be able to edit the clipping spline without it affecting the layout of the array.
I hope that helps, please let me know if you have any further questions.