Hi, drrdf. As to the autostart files and directories, I have a custom LXDE setup so most of my autostart files/directories do not match to the default. The one directory I am certain matches is /home/[username]/.config/autostart which contains .desktop files of programs that are autostarted. You can delete any program file from that directory that you do not want autostarted. Sorry I can't help more.
This may sound strange, but you might try completely removing numlock then reinstalling to give numlock a new configuration. My thoughts are: numlock came preinstalled and any programs having dealings with numlock knew that (for example, Lite Tweaks and LightDM). If you completely remove and then do a new install of numlock, the mystery setting that keeps turning it on might dissapear, note I said maybe
Command to completely remove numlock: sudo apt-get purge numlock
(Purge removes all configuration files for that package.)
To error on the side of caution, I would reboot so other programs that have dealings with numlock see that it is no longer installed and adjust accordingly (hopefully).
Now reinstall numlock: sudo apt-get install numlock
Then go to Lite Tweaks and ensure that numlock is turned off.
I cannot promise this will work, but at this point, almost anything is worth a try. When I was using straight up Ubuntu, I did this once or twice for some programs and it actually worked, but then other times it didn't seem to change anything. Please let us know.
Good luck, skippy95