I can't believe we seem to be the only ones having pen issues since kitkat.
Mine was working again there for a little while, but just now stopped while I was in the middle of using it. When that happened, the screen wouldn't even respond to touch input. Home and power buttons worked, but nothing touch/pen/hover based. Once I turned the screen off and then back on, I had touch/hover input again but not pen. Even though the "pen out" icon on the status bar was there still, and went away when I put the pen back in the phone. Doing so did not make the pen work again though.