Then you have no broken or missing packages, at least none Synaptic can detect.
Ever since I installed KDE 4 my numlock light goes out the first time I touch a modifier key (Shift, alt or Ctrl), so that seems to be normal, albeit obviously a minor bug of some kind. If changing BIOS settings has introduced more problems I would change them back. If the numlock light going out bothers you, you can always bring it on again by pressing the numlock key twice, though it will only stay on until the next modifier key is pressed.