I have used MATE from time to time with Debian 9 and other distros and have not encountered this.
Try booting to a
Live CD of Debian with a different DE and seeing where the problem exists in the live environment. If it doesn't it may not be a MATE problem.
You could also try installing a different DE or a window manager to your Debian 9 system and testing with it.
This last is a complete shot in the dark, but have you tried blowing out any dust and debris that might have collected under the keys with compressed air? I doubt that's the problem, but that option easy and quick.