FWIW, Sigil on macOS and other platforms has the same issue with its Find and Replace and the bug is internal to Qt where it does not properly restored saved state and geometry of docked windows when reopening. This bug has been long reported but never really fixed by Qt.
To work around it I had to:
in close event before saving state and geometry, save fact F&R was open or closed, close it, then save main window state and geometry.
When opening in ReadSettings restore geometry and then after final resize is done reopen F&R if it was previously open.
This is a horrible hack but I could not see a better way.
Looking forward to see what Kovid comes up with here as I am out of ideas.
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