If the troubleshooting in this thread does not help. I recommend letting a service technician have a look. Send your full model code and serial number via private message to get started.
I have found out the issue really comes from the Bluetooth software installed in the laptop. You may want to re-install Bluetooth and that should at least resolve the problem with the S-pen temporary. The problem my re-surface later since the "bug" is really with the Bluetooth software itself. Samsung will need to look into their Bluetooth system software installation and "fix" the problem once and for all.