No magsafe or any case magnets, nothing like that correct?
Weird. Has it always been like this? If not when did it start, like how long ago? Trying to tie it to an update or something like that. Which brings me to my next thing which is clearing the phone partition cache. You've cleared the cache for the game app, I don't think there is any way to clear a cache associated with the S-Pen directly so the big cache for the device would be as close as I think you could get.
You could uninstall the game and install it again. I imagine it saves your progress/earnings or whatever, so you wouldn't lose anything as long as you have an account for the game. This might be more for if this has always been an issue but I guess it could also be if a game update started this... Just something wonky happening software wise.
The only other thing that comes to mind is installing Pentastic. I don't know that it changes much with anything but maybe it adds something.
@mustang7757 do you have Pentastic from GoodLock installed by chance? If not ignore this I guess.