Around April 10, 2012 Microsoft updated the Internet Explorer 9 installers with a broken version. Until this issue is fixed, your safest bet is to use the older installer here, then update with Windows Update (just do not perform an initial install from Windows Update).

See the Microsoft Answers thread here: http://answers.microsoft.com/en-us/windows/forum/windows_other-windows_update/windows-server-2008-r2-sp-1-internet-explorer-9/ac2ed42f-7faf-4731-8af9-7a50d946138a
Jonathan Sahagun found a direct link to the previous, working version of IE9 here: http://www.microsoft.com/download/en/confirmation.aspx?id=23332

There are two solutions – probably the safest solution is to uninstall then reinstall an older version. The alternate solution is to make a couple registry changes.

Symptoms

After this bad version of IE9 is installed, you will be continuously prompted by Windows Update to install Internet Explorer 9 – it appears as though it cannot tell you already installed it.

If you attempt to install it again, the update will fail (with Error “Code 9C48  Windows Update Encountered an unknown error”), but it will continue to repeatedly offer the update:

Additionally, there is a conflict between the version embedded in the files, and the version reported by IE:

To see the version conflict, browse to C:\Program Files (x86)\Internet Explorer\iexplore.exe, view the properties, then the details tab, and note the Product version number:

In my case, it is 9.00.8112.16443 (file version is 9.0.8112.16443)

Now, within Internet Explorer, got to Tools –> About Internet Explorer

The version doesn’t match – 9.0.8112.16421
(Note: On my other system where IE9 was installed before April 10, this is the version number on both the files and in the program)

Solution #1 – Confirmed, Probably supported

If you haven’t already installed IE9, use the following link to install it: http://www.microsoft.com/download/en/confirmation.aspx?id=23332

If you already installed it: uninstall it, then reinstall using the linked version.

If you have installed other applications since installing IE9, this may break things. I have also seen the uninstall leave IE in an inconsistent state… so naturally I sought out an alternative.

Solution #2 – Quicker, safer, riskier

It looks like this version conflict is a registry setting:

In HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Internet Explorer  (and also HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Internet Explorer), svcVersion should match Version and W2kVersion. Change it to 9.0.8112.16443

And Viola, IE9 reports the correct version, and Windows Update stops offering the Installer.

Hopefully Microsoft will figure out the mistake soon (as of this writing it has nearly been a week) fix the installer, and fix Windows Update to recognize and remedy the broken installs.