How to reset all gnome-tweak-tool settings to defaults

Actually, you can simply open GNOME-tweak-tool (in GNOME), and click on its icon in the top panel. You should see an option that says "Reset to Defaults."

Here's a super easy solution.

Reinstall gnome-tweak-tool with

sudo apt-get install gnome-tweak-tool

Run Tweak Tool

choose Windows and change the setting for Windows action keys from Disabled to ALT

This will undo the change you made and make the buttons work as they did previously.

I followed the jrg guide how to reset GNOME to its defaults. I simply had to execute this command in terminal:

rm -rf .gnome .gnome2 .gconf .gconfd .metacity .cache .dbus .dmrc .mission-control .thumbnails ~/.config/dconf/user ~.compiz*

And Unity windows buttons started working properly.