You can modify the minimum panel size and the margins. Right-click on the vi's icon located at the upper-right corner, and select "VI Setup".
As a trick that work for me: At design time, resize and position the front panel as you like, the same way you can manipulate any windows screen. Then change something in the vi so it is edited (you know a vi was edited and hasn't been saved when the title of the window has an asterisc) Then, save your vi. The new appearanc of the window will be saved too (unless the settings were already modified, as explained in the previous paragraph.)
Also, as Gorka mentioned, check for controls or indicators out of bounds.
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