close each one... open them fully. On the toolbar > Exit

This situation is usually the result of right clicking a folder and selecting open in a new window. Once you close using the relevant X they should stay closed.

Didn't work. If I click EXIT on one of the 4 windows, they all close. Then all of them re-open when I open Thunderbird.

Interesting thing - if I close one of the 4 windows with X, actually 2 of them minimize to the system tray (lower right corner). Then if I click X on one of the remaining 2 windows, both of them minimize to system tray. If I click EXIT, either in one of the windows or in the system tray, all 4 of them close at the same time.

Alt+F4 closes an active window. Can you close out the extra Windows that way?

Didn't work either. Alt+F4 minimizes windows one by one to the system tray and then it's all over again.

Try pressing F10 to enable the main menu bar and use the option on the file menu to exit.

Tried that already. Didn't help either.

Any other suggestions? I tried reinstalling the thunderbird. That did not help either..

Do you still get multiple windows if you start Thunderbird in its Safe Mode? We know of some add-ons having caused similar issues.

Hold down shift whilst starting Thunderbird.

It did work! Sweet! Thank you, Zenos! :) At first it did not work. I chose "Disable all add-ons" and then "Reset toolbars toolbars and controls". It still opened 4 windows. Then I right clicked Thunderbird icon in the task bar, clicked 'Close windows' and the next time it opened only one window like it's supposed to. Thanks again! :)