Tive o mesmo problema chato. Achei isso:
I went on the hunt for a "fix" for this annoyance, and here is how this "feature" can be turned off and allow for the toolbox to be hidden behind the image window. Open GIMP (Applications > Graphics > GIMP Image Editor). With Gimp open, From the Edit menu, select Preferences. Locate and select Windows Management from the left hand navigation. In the Window Management section you'll find "Window Manager Hints." Change both the hint for the toolbox and other docks to "Normal Window" and click OK.
You will be prompted to restart GIMP with the following message:
"You will have to restart GIMP for the following changes to take effect:
toolbox-window-hint
dock-window-hint"Click OK. Close and reopen Gimp. The Toolbox will now be able to be hidden behind the main window.