This bit of info is a lot more helpful than the previous "can't click", thank you. Although sadly I can't reproduce this behavior, if I set the game to windowed I can click the menu button just fine.I am struggling with the settings icon that's in the hotbar when "playing"...I said in my previous comment that when i try to click on the settings icon, the character i'm controlling follows the cursor that's in the corner of the screen (where the settings icon is) and settings doesn't open.
Does clicking on the other buttons in the UI work? Maybe the clickable area is offset from the visual buttons in some way.
Does this always happen when your game is set to windowed or only if the game's resolution is set to your fullscreen resolution?
Regarding resolution when alt+enter: Seems like the game sets the resolution to your native fullscreen resolution when you enter fullscreen mode, but doesn't change what is displayed in the options menu, so when you set it back to windowed, it stays in fullscreen resolution. And since the top bar always has to fit in the screen, the bottom of the game will always be lower than what your monitor displays.
To get back to a smaller resolution, change it in the options to anything else, then back to your desired resolution.
As a workaround to not being able to click the menu button, try seeing if pressing the Tabulator key on your keyboard opens it - it's bound to that button per default.