My Latte Dock also got messed up! At first, only the first two applications and the application menu on the dock were clickable, so I decided to kill
/usr/bin/latte-dock and remove
~/.config/lattedockrc to start fresh. It didn’t work. Not really. The default dock does pop up when I move my mouse over to the bottom, but it doesn’t respond to my clicks. Not even right-clicks so I can “edit dock”. I tried using another layout and starting with an empty layout and an empty panel. The panel does respond to right-clicks, but after tinkering with the settings, it becomes unusable again.