The Vassal player seems to store a window’s dimensions and position but not the zoom level of its contents. Perhaps, zoom level could also be stored/restored between module starts ?
Example, C&C Napoleonics module. Start scenario, press F3 to display dice tray window. Size is accordingly - this example is shrunk to the minimum zoom level and the window then re-sized:
After a restart of the module, when the show window hotkey is actioned, the window appears at the same position and dimensions, but the contents are zoomed to default: