Disk CleanUp on vista Ultimate can damage the operating system. Not sure on other versions have not tried them. Once you have damaged the OS doing this there is no repair except for a fresh install of your operating system. So to fix this problem you can use one of two ways.

First way, download this unzip double click, click ok to add to registry.

http://www.winhelponline.com/blog/wp-content/uploads/2008/02/cleanmgrfix.zip

Or you can do it manually.

Open Regedit (start - run - regedit) and go to:

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\explorer\VolumeCaches

There you will find 4 keys called Windows error reporting.
Now if you look closely you will see that one (or more) is missing the Folder string.
Now, lets get to fixing it.

If you are in the " Windows Error Reporting Archive Files " key

Right click - New - Expandable String Value.

Call it Folder and use the following entry:

%USERPROFILE%\AppData\Local\Microsoft\Windows\WER\ReportArchive

If you are in the " Windows Error Reporting Queue Files " key

use: %USERPROFILE%\AppData\Local\Microsoft\Windows\WER\ReportQueue

If you're in the " Windows Error Reporting System Archive Files " key

use: %ALLUSERSPROFILE%\Microsoft\Windows\WER\ReportArchive

and if you're in the " Windows Error Reporting System Queue Files " key

use: %ALLUSERSPROFILE%\Microsoft\Windows\WER\ReportQueue

From what i have read it has something to do with the cleaning of the error reporting. I have also read where the disk cleanup causes programs files to disappear.