VI windows will come up the same size as they were saved. What you may be experiencing is that they are not saved if a windows size or position change is the only change. Even if you press CRTL+S or use File -> Save.
One way to get around this is to "bump" something on the front panel, which makes LabVIEW finally think that something has changed. One way that I do it is to select some front panel object, move it a pixel with the arrow keys and then move it back. There is no noticable change, but LabVIEW now thinks it is different and will save it when you tell it to.
Hope that this helps,
Bob Young
