How can I disable my Caps Lock key on macOS Sierra, without it resetting after a reboot?
It could be a problem with file permissions. Try this command in the Terminal (a built-in system tool):

chmod -RN ~/Library/


It resets permissions for your user Library folder. When the command is done executing, reboot. Change the setting and then reboot again, and see if the setting persists.

If it didn't work, then try this command:

chmod -RN /Library/


Yes, there is a difference: it resets permissions for the system’s Library folder.

Then reboot and change the setting as mentioned before, and see if it persists now.