Ultimately the problem is that the windows along the right side all have minimum heights, and if the combined heights are larger than the height of your display, they won’t fit and weird things happen.
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You can dock all the windows together, as shown here: Update to 9.10 and 9.11 to big window "Laser"
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You can reduce the size of the toolbar icons in Edit > Settings, which frees up some space for the side windows
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You can dock your palette window vertically along the left or right sides.