I was having the exact same problem (2016b, OS Sierra), which appeared when I had entered full-screen mode while connected to projector. In MATLAB click on new app designer script or open existing mlapp file, icon should appear in the dock. Then Menu->Enter full screen, app designer will show up, if not, swipe on your trackpad until designer window pops out, then reset it by closing MATLAB Window from the top menu. Worked in my case. Btw I tried changing the matlabpref.mat as suggested by Sean, it did not work itself, but there still might be a correlation with my solution as I didn't change the setting back.