Moving between open windows and cursor doesn't work

I have several open windows from several programs.
If I click on window 1 in program A, and then click on window 2 in program B, I expect the mac to switch to that window in program B.
But many times lately, in Tiger, that does not happen. I can click on the window, and the cursor does not work. Nor does the menu bar change. I can go back to window 1 and the cursor still does not work.
Only when I go to the dock, and click on the program icon does the window and cursor work properly.
This happens in Tiger. I don't recall having this behavior in any older OS X, OS 9, or other older version either.
This has happened on my iMac G5 and G4 tower. Is this a known problem?

This happens since I started using the Mighty mouse on both computers.

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