Chattering nearly always has to do with intermittent connection. The question here is, what is causing the intermittent connection. I would start at the switch and work back. If it isn't the switches themselves, the next thing I would assume would be that a trace is cracked. I would first start checking the matrix lines associated with the keys that are the biggest offenders. Once you locate the crack, use a mod wire to bridge it.
I don't know if I would skip from the switches straight to the micro-controller. That has disappointment written all over it.
PS:Also, if it is a crack in the trace, you probably cannot see it without a microscope, but gently flexing the keyboard will help, since the trace would only disconnect anyway when flexing when a key is being pressed. It may have to be located logically by keeping a log on which keys are chattering, then label them with the matrix lines until you find the correlation. If there is no correlation at all, then the micro-controller is bugging out.