If you are using a case with a magnet in the clasp, it will interfere with the S-Pen detection in that area. Try removing any cases you use and see if that helps. (Not sure, you may have to leave the phone for a while after removing the case).
Glad that fixed it for you. I suggest looking for an alternative case - see some of the recommended ones on the forums here. Personally, I stick to the offical Samsung ones, or recognised brands like UAG etc. I always stay clear of cases with magnets for Note phones, as this has always been an issue. Case manufacturers should be aware of it by now! The only place a magnet is acceptable is if it's on the back side of the phone away from the screen.