I did... And it turned out it was because of the magnet in the cover I was using. The magnet that seals the cover, messes with the phones ability to detect when the S-Pen is in the phone, and it also makes the pen not work correctly in general, like when writing normally or trying to do gestures and screenshots through the pen.
Remove your cover, if it uses magnets to stay closed, and see how your S-Pen magically starts working again.
Remove your cover, if it uses magnets to stay closed, and see how your S-Pen magically starts working again.