Hi,
Let us try to download and install Internet Explorer 9 manually in Clean Boot environment.
1. Download the installation file of IE9.
http://windows.microsoft.com/en-gb/internet-explorer/downloads/ie?SignedIn=1
2. Boot into Clean Boot environment.
http://support.microsoft.com/kb/929135
3. Please try to install IE9 again. If you still encounter the error message during installation process, please collect the screenshot for me or provide the detail error message.
In addition, providing the windowsupdate.log file will be helpful.
Kim Zhou
TechNet Community Support
