Recently I had to re-start my laptop. After rebooting and logging into the MATE desktop environment the screen had 100% backlight, and the function keys to change the backlight did not work anymore. Changing the keyboard backlight did also not work anymore.
It turned out that mate-power-manager is responsible for handling the keys and changing the light level. After starting it manually, the keys work again.
I have no idea why the power manager does not start anymore automatically, but I'm glad that I can work around it. This is MATE 1.6 on Ubuntu 13.10.