We can have this trouble when you use HB on multiple computers with the same settings (with Dropbox for example).
If you have a bigger resolution on the first computer and you open the settings outside the resolution of the second screen, you won't see the window.
To solve the problem and as BobbyNewhart said, maximise the settings. Then press the top of the full-sized window and drop it anywhere on your screen. Normally, the settings window will take its normal size.