I've now followed the instructions from your original post again.
I can still reproduce the problem with WinSCP 6.3.7. But it works for me with WinSCP 6.5.1.
Do you happen to have multiple displays maybe? Does it possibly happen on one of them only? Do you have scaling enabled in Windows?

Looks like it's broken again in 6.5.1.

Guessing something to do with
Issue 2366 – Monitor placement and maximization is not remembered on monitors with different scaling than the primary one

Thanks for your feedback.

Thank you. Success.

The dev build successfully fixes this issue. Well done!

Thanks for your report.

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.