[JKT]

Note, I normally only ever have one window open at any time in my workspaces and its position is fixed by the snapshots I take.

However, I've just tried to reproduce your issue. I don't see the gap between top of window and menubar, but instead see one introduced at the left hand side of the window instead! That is, if I have open a single non-maximised window, save its window size, close it then open a new one, it isn't shifted downwards by 21px or so, but is instead shifted to the right by what could be a similar distance.