I just tried removing MATE and re-installing it but only in part with:
sudo apt-get install mate-desktop-environment-core
After logging in, they keyboard all worked apart from r which is taking a screenshot.
I deleted that shortcut key using the Keyboard Shortcuts utility and then r started working again.
Then I installed more of MATE with:
sudo apt-get install mate-desktop-environment
After that, r was was still working, but now b and n don't work, these are the brightness keys, and they're not in the keyboard shortcuts list.
Any ideas?