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.
The hidden Modal window will have something like this:
Now, the question is how do you close this if you can’t see it?
Open “Task Manager”, look for SSMS and then among the multiple options, choose the “message window” from above
Right-click and switch to it
..and close it!
This problem is annoying enough that knowing this solution may help you not lose your open work!
SQL Jana 
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