The window layout is an application setting, not a project setting. The layout is not saved in project files.
I do know that some machines have a problem with the initial sizing of the layout on pI3 for Windows — it seems that the stage window width is reduced by some amount at startup.
I usually use layout 1 as my preferred layout, so when I start pI3 I automatically hit Alt-1 to arrange the layout I need.
Just to be clear, there is absolutely no connection between stage size and stage window size (layout). They are independent. I can create a 2000 x 2000 stage size, but make the stage window 100 x 300 pixels either manually resizing or via the layout functions.
Alan.
wondertouch