I am not sure if run into this but I do often enough on my SSMS 17.9.1 version – suddenly, the SSMS window will not register any mouse-clicks although it will seemingly look fine. The reason is because there is a Modal Window somewhere hidden. Sometimes, ALT-TAB followed by ESC will do the trick but not always. In the beginning, when I did not know about the modal window, I used to kill SSMS and restart it but you don’t have to.
Click through to see how to do this and save yourself a task killing.