Another defenestration happened in Prague in the late 1940's, sometime after World War II. In this case, the victim was Prime Minister Jan Masaryk, the son of the first President of Czechoslovakia, Tomas G. Masaryk.
Jan Masaryk was a man of democracy, American style (his mother was an American). Because of that he presented a serious problem to the rise of power of the Communist party, and was, hence, defenestrated from his office which also was at the Hradcany castle, just like the first defenestration of Prague.
Masaryk's murder was covered up as suicide and would probably continue to be believed as such if not for the attempt to re-establish democracy in the spring and summer of 1968. At that time, someone (sorry I don't remember his name) published theretofore unknown facts about the alleged suicide. Shortly before it happened the organizers of the defenestration somehow arranged for everyone but Masaryk to vacate the building. The phones mysteriously stopped working before the murder, and were just as mysteriously fixed afterwards. The article describing the events went to much greater detail, alas, this is all I remember. I was 18 at the time, and 1968 was quite a hectic year.
However, I do remember that the author of that article demonstrated quite clearly (well, at least to me back then) that Masaryk's death was no suicide but a murder by defenestration organized by the Communists. Considering that the Communists of Czechoslovakia had no qualms about killing anyone who stood in their way, and that Masaryk's "suicide" was very convenient for them, I still believe the article was accurate and that Jan Masaryk was indeed murdered by defenestration by Communists.