Try pressing alt + F4 to just close one of the windows. What version of Thunderbird are you using? This was a problem with some older versions about a year ago.

Version 31.7.0 and it did not work alt + F4, it did noting but highlight File tab.

Interesting. alt+F4 is a standard windows shortcut that closes the active window. If there is only one window open a dialog box usually opens asking if you want to shut down Windows. I have never seen it move to the File menu.

You are using the F4 key and not f and 4? Alt + f moves to the File menu. Pressing the 4 after that is just finger exercise.

Maybe someone else will have a suggestion for you. This is the first I have heard of dual windows in the newer versions.

No I'm using the right key.

OK. I have to trust you since I cannot see your keyboard, but it is suspect that alt+f opens the file menu like you describe.