I was having this problem in win2k, with the clean manager hanging at scanning compressed files and it wouldnt go anywhere even after buttloads of time.
So i found a fix
Open regedit. Navigate to:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\Curr
entVersion\Explorer\VolumeCaches
Delete the entry "Compress Old Files".
Now cleanmgr.exe will work! You can still compress files manually, but cleanmgr.exe will not have the capacity to automatically compress old files after you make this change.
compliments of http://www.tech-forums.net/computer/topic/798.html
CleanManager hanging with 99% CPU usage?
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CleanManager hanging with 99% CPU usage?
Gone for good. But never say never