The biggest frustration with Gimp 2.6 has been that pesky toolbox window always in the way over what I'm working on. Turns out it's easy to make it act sanely. Try this: Go to Edit; Preferences; click Window Management; and under Window Manager Hints, change "Hint for the Toolbox" from "Utility Window" to "Normal Window." Then click OK.
I would have thought this would be called "Always On Top" (Gnome has an Always On Top setting, but it doesn't help here) or something useful. "Utility Window" doesn't explain that it's an "Always in your way" window... someone needs to find better words!