MAXScript remembers the state of its desktop (the location of active Editor and Listener windows) when you exit 3ds max and restores this state when you restart MAXScript. Any MAXScript Editor files missing when you restart will not have their windows reopened.
The desktop state is stored in a file called maxscrpt.dsk in the 3ds max executable directory. You can rename this file and replace it if you want to keep several desktop setups configured, or simply delete it so the current desktop will not be restored.