Dunno what it is about 999 clutches,but they seem to need bleeding regulary.My theory is a problem with the master cylinder.There never seems enough fluid in there while the bike is on the side stand.Yet once the bike is upright the fluid level is on the max mark.Maybe air is getting in there?........who knows?!
As Nelly says,you may need to bleed the clutch.The easiest way is to do it from the master cylinder.Make sure the bike is upright,ie on a paddock stand,and remove the master cylinder cap.Inside you will see a 6mm headed bolt.Undo this slightly and GENTLY pump the lever.You should see air bubbles coming out.Once the bubbles stop,hold the lever in and tighten the bleed bolt.Refit the cap and test the clutch.Should work ok.