A small update is now live with improvements to windowed and fullscreen behavior.
Window position and size are now saved and restored correctly across multiple monitors, including secondary displays and wide window layouts that span screens. Fullscreen with F11 has also been improved and now uses the resolution of the display the game window is currently on.
The Settings menu has also been simplified. It now includes only Fullscreen (F11), Window, and Properties, and the old fixed-resolution shortcuts tied to the removed menu items have been removed.
Thanks to PaTcH and Castro for reporting these issues.