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I don't know if this is what the OP is referring to, but I've experienced the same - or a related - problem myself.
On my PC, at the window size I run Calibre at, the menu bar isn't quite wide enough to display the "Preferences" button. If I click the ">>" at the end of menu bar to make it appear, "Preferences" appears at the left side of a second row of the menu bar. No problems there.
The problem is that, of course, my mouse is at the right side of the window (having just clicked ">>") and "Preferences" is at the left side of the window, so I have to move the mouse across to the left to get to it. About half the time, during the process of moving my mouse across the "Preferences", the second row of the menu will spontaneously disappear again, and I have to repeat the process all over again. It sometimes takes 3 or 4 attempts to successfully get to "Preferences" without it disappearing!
It's a trivial thing, but it's something that Calibre has always done for me.
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