Well, compared to the default set of Preferences, the ones you’ve changed in the note input category are:
- By default, specify pitch Before duration
- Specify accidental, rhythm dot and articulations Before inputting note
- By default, enable note input using the mouse is off
- Enable note pitch and rhythmic position editing using the mouse is off
So the only thing I can suggest is to try changing those values one at a time and see which one makes it start working again.