I am having the same problem in the 787 right now. I had this problem before, although not even the MCDU was working that time. The solution then was to open the ATC window and move it to the center of the screen, then close it. Although this has not worked this time. Strange cause the 787 was working fine for me for the past couple updates (and for most of this update).
UPDATE: I had a memory stick connected to the computer, I took this out and it appears to be working after a few minutes. Not sure if it was because of this though.