In some ways I'm surprised that Android seems to demonstrate the same sort of issues as Windows. Things like needing to reboot occasionally because the system has become unstable and/or bogged down. Mysterious processes in the background that are chewing up CPU time and you have no idea what. And a boot up process that gives you a home screen fairly quickly but still needs another couple of minutes for all the various startup processes and apps to settle down.

If background activity is the cause for the pen "stuttering", then a reboot and/or waiting a few minutes should restore the pen to full responsiveness.