As I noted in my answer to How do I make the Caps Lock key a third Shift key? The keyboard indicator lights seem to go out of sync at boot on Ubuntu 16.04 For example Set your BIOS to Num Lock ON and boot. Keep an eye on the indicator throughout the boot and login process. You'll note that it goes out and has to be tapped twice before it accurately reflects the num lock status. Why is this and how can this faulty behavior be resolved.
One of the systems I'm experiencing this on doesn't have an option to turn off the numlock at boot. The other one does and even when NumLock on at boot is disabled the indicator light is still out of sync.