Application windows do not respond - help please!

Hi everyone
At first I should say that I did search for this topic in search forum section but all of the cases related to freezing windows app. do not match my problem.
So recently something strange occurs: my app windows freezes (I mean I can't close them nor move them) while everything else works (app is responding) - I can quit it using dock. And when I open it again it appears in strange place like the edge of my screen. It happens with very simple apps like: Finder, Safari and iTunes.
The whole thing started the day before (I don't know if it could be related to this) I have installed cocktail - to clean my macbook and quicksilver.
things I tried: I verified and repaired permissions using Disk Utility. I have also verified Disk (it showed me minor error with disk header) and redpaired it using installation disks.
An the problem still occurs!
Please help!
wk
iMac Intel 2 GHz - 1GB RAM, Macbook Intel DualCore - 2GB RAM (black)   Mac OS X (10.4.9)   Tiger, iLife '06

I have a similar problem, but for me the unresponsive application (iTunes is doing this as I write) cannot be quit using the dock. Initially, when it first became unresponsive, The arrow still appears under its dock icon to indicate it is there, but when I right-mouse the icon, it goes into the state as if the application was not running (no arrow). Right mouse shows "Open" as an option. I can see the app right there...
Activity monitor sees it and allows me to quit it (gracefully - no force quit required) then the app will launch and All is well... until another app exhibits this strange behavior. I have seen this happen to iTunes, Safari, and Finder most often.
At first I thought it had something to do with safari 3 beta, so I backed that out. Only other things I can think that have changed on my system since when it was in working state was Parallels Desktop 3.0 and the 10.4.10 upgrade. It has been misbehaving since June (through several security updates etc).

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