I think Dennis's answer is right on the money, but I also wanted to point out that you can programatically set the postion of the front panel. You do this with property nodes. The trick is to put the controls where you want them and use the postion property on the controls to write their location to an indicator. Now you change the property node to write and your indicators to contants and put this code in the beginning of your VI. This way everytime you run the VI, the controls will be exactly where you want them.
Jeremy