Are you in Gnome or KDE? Which tool windows are you having trouble with?
Are you talking about the tools hiding dialogs underneath it? Currently there are a couple workarounds. You can either 'dock' your tool palettes to the edges of the screen or you can simply move them out of the way for most windows.
If you have a focused window that's hidden underneath another window, you can press Esc to cancel the dialog. Then move the palettes out of the way and try again. If this happens often, dock your palettes.
Hope this helps. If not, give me an example.
Would be a reason for me to upgrade (even pay a new license) if this works for office tools too
You can pledge dollars to any application you'd like to see improved, or vote with your licenses!
Peace
Chris