Does disabling "System Integrity Protection" in El Cap cause shutdown/restart/logout issues? I have an older M-Audio Firewire audio interface that I use with my Mid 2011 Mac Mini. It's running OS X El Capitan 10.11.6. M-Audio never made drivers for this version of OS X, so I have to disable "System Integrity Protection" for the audio interface to work. I do this by booting to recovery > Terminal: csrutil disable then rebooting normally. 

However, I have an issue where I cannot logout, restart or shutdown "cleanly." What I typically do is run the sudo restart now command to reboot, or sudo pkill loginwindow to log out. EDIT: What I mean here is OS X (El Cap) is getting "stuck" (just hanging indefinitely) when I try to either a.)logout b.)restart or c.)shutdown. It just does not work, so I use terminal commands to force it, but I want to stop having to do this. 

Could this issue be related to disabling SIP? EDIT: I have disabled SIP, no change. They are not related.
This was a software issue, after all. Once I upgraded to macOS High Sierra I was once again able to reboot normally, regardless of SIP status.