Keyboard LEDs and multiple screens problem. (mate 16.10 beta)
This is, in fact, an old bug. It's present in both Ubuntu Mate 16.04 and Mate beta 16.10.
In order to reproduce, open MATE Tweak and mark "Enable keyboard LED".
What I do is unlock the Date, LED indicator items in the Panel and reorder the way I like, then, "Lock to panel" again when I finish. The problem show off if you are using an external monitor. Seems like the LED indicator is not aware of resolution changes and "breaks" the order you gave it before, even when it is locked. As a result you must reorder the Panel items every time.
Using Daily Build from 23/sept/2016. Ubuntu Mate 16.10.