Are you using two monitors ? That might be a problem.
I would try this.
Go into multi-window mode.
Reset the windows to default positions Edit -> Preferences -> Window Management -> Reset Saved Window Positions to Default Values and restart Gimp.
That should give toolbox+tool options on the left - the main Gimp window - layers / brushes etc on the right and all fairly close together. (Then into multi-window mode, if not already there.)
Then you can drag around the docks, resize the main window, set up the way you want.
Back to Edit -> Preferences -> Window Management and there just under Window Positions is a toggle for Save window positions on exit toggle that off.
Now click on Save Window Positions Now , OK Preferences and restart Gimp.
Gimp will start up in that layout.
If you dont like it it then toggle that Save window positions on exit on and Gimp will now remember whatever is last used.
I would try this.
Go into multi-window mode.
Reset the windows to default positions Edit -> Preferences -> Window Management -> Reset Saved Window Positions to Default Values and restart Gimp.
That should give toolbox+tool options on the left - the main Gimp window - layers / brushes etc on the right and all fairly close together. (Then into multi-window mode, if not already there.)
Then you can drag around the docks, resize the main window, set up the way you want.
Back to Edit -> Preferences -> Window Management and there just under Window Positions is a toggle for Save window positions on exit toggle that off.
Now click on Save Window Positions Now , OK Preferences and restart Gimp.
Gimp will start up in that layout.
If you dont like it it then toggle that Save window positions on exit on and Gimp will now remember whatever is last used.