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I have added this issue to the tracker:
Issue 2305 – Open window maximized when closed while minimized from maximized state

I'm sending you an email with a development version of WinSCP to the address you have used to register on this forum.

The Main Window Opens Unmaximized If Closed from System Tray on Transfer completion

That is enabling: "Once Empty > Disconnect Session" and minimizing the window to the system tray while the main window is maximized.

Settings:

• Preferences > Environment > Uncheck (Disable) "Closing sessions when exiting application" and "Exiting application on operation completion"
  
• Preferences > Environment > Window > Check (Enable) "Minimize main window to taskbar status area (system tray)"
  

I'd expect main window to open up maximized again on next session since the window was maximized the last time before it was minimized to the system tray.

1. Enable / Disable the options above as listed
   
2. Start a large enough background transfer that takes a min or 2
   
3. Enable "Once Empty > Disconnect Session"
   
4. WinSCP main window should be maximized
   
5. Minimize the WinSCP main window
   
6. Wait for transfer to complete and for WinSCP to close as expected.
   
7. Rerun WinSCP and notice the main window is no longer maximized.