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OK, I'm still having problems with an HP dv5000 (about which my only advice is "run away").
I'm posting this here instead of under laptops becuase the behavior manifests both with the touchpad and with the USB mouse, so I'm thinking it is more generic.
So, what happens is, say you launch a program from a blank desktop. The new window opens up fine. The mouse, however, seems to stay focused on the desktop behind. I cannot click in the new window, and if I move the mouse to a part of the screen where I know there is a desktop icon (behind the new window), it brings up the tooltip for that icon!
You've probably already tried this, but just in case... What I would do is find the function for altering mouse behavior, in whatever window manager you're using, and try various settings. In some WM's there is an option for automatically moving the mouse focus to the window as it's raised. And there are many other combinations and possibilities.
And no, I have never seen this problem myself. It sounds both interesting and very frustrating. Hope you can fix it soon.
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