Follow these steps to reproduce the bug:

1. Enter a new keyboard-shortcut.
2. Double-click the entry you created.
3. Hit enter or click ok
4. sometimes steps 2 and 3 need to be repeated once or even several times. Repeat those until the wrong windows appears: instead of the command window the shortcut window
5. now enter a the same shortcut you used before
The entry will dissappear.