My key words:
gimp snow leopard terminal 10.6 window focus
I knew the problem was in X11. In previous versions of Mac's OS with Gimp, I could rely on typing a terminal command. I knew the problem was that in X11 with multiple windows, when switching from the tool window to the canvas window to the layers window one click was required to focus X11 on the window the second click actually made the selection on the window.
1) With X11 open, click X11 - Preferences.
2) Choose the Windows tab.
3) Place a checkmark in the "Click-through Inactive Windows" choice NOT the "Focus Follows Mouse" choice.
4) Close the window.
5) Repeat on the rest of the classroom machines.
*** UPDATE ***
My home computer runs Leopard (10.5). I was having the same problem, but the version of X11 does not have the Windows tab.
A little more searching with the keywords
gimp 10.5 terminal window focus leopard
...got me to this page.
To fix it in X11, copy and paste the following code into the Terminal program.
defaults write org.x.X11 wm_click_through -bool true
Start Gimp and enjoy having the focus of the mouse work!