All windows inactive while apps keep running, but I can't interact anymore

Dear forum,
From time to time (and increasingly frequently) I experience an odd kind of "freeze": Suddenly the window I working in turns inactive. I can click on any window, no matter what application or bring them to front using Exposé, but as soon as I click on something inside a window, in order to work there, it turns inactive again. This is even true for the "shut down" window.
While this is happening, the applications apparently keep running. Once when this happened, iTunes kept playing songs and even changing tracks, only that I couldn't stop it or chnage tracks manually.
I repaired permissions several times, without any effect.
First I suspected any side effects from Growl, which I had freshly installed at an early occasion of this issue. I have removed Growl from my harddrive since then, but the problem persists.
I checked the console.log and the system.log after the latest "freeze", but there were only the usual startup messages from the reboot.
Has anyone ever experienced something similar? Please help, it happened twice today!
Thank you,
Matthias
iBook G3 Mac OS X (10.3.9) 700 MHz, 640 MB RAM

Try booting into Safe Mode. This will take quite awhile longer than a normal startup because it does a file check and repair of the hard disk.
You will see your normal desktop. Once completely started up in Safe Mode, restart normally, and go to Applications > Utilities > Disk Utility. Click on the top hard drive icon in the left sidebar and note the S.M.A.R.T. status at the bottom right of the pane. What does it say?
Select the named boot volume in the left sidebar, and repair permissions on it again.
See if a little hard drive maintenance helps things out.

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All windows inactive while apps keep running, but I can't interact anymore

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