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Internet Explorer 9 not showing as not installed when using Windows Update - Error: Code 9C48 Windows Update encountered an unknown error.

Update:10-11Source: network consolidation
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I built a few new Windows Server 2008 R2 with SP1 VMs today and ran into a problem where Windows Update is not detecting the fact that Internet Explorer 9 is already installed. Internet Explorer 9 keeps showing up as an available update when
using Windows Update. When I try to install it as a test I get the error message: Code 9C48 Windows Update encountered an unknown error.
My normal build procedures include applying all the patches for the OS prior to any other work on the servers. The way I like to do the patching is to do every update other then IE9 in the begininng and once all the other updates have been
completed, install IE9 and then patch it if there are updates available. I followed this procedure on every build for the last year and I have not run into any issues until today. The only difference today is the latest patches that were released yesterday
April 10th, 2012. To test the theory that it may be one of the latest patches, I reinstalled Windows from scratch making sure to format the disks and then I installed IE9 right after the OS install without any other updates. Once the
server was rebooted, I checked Windows Update and Internet Explorer 9 still showed up as update (Not the Cumulative Update which normally shows up after an IE9 install) and yes, I did make sure to click the 'Check for Updates' link before I looked just
in case. My next test was to patch a couple of the servers I had built prior to April 10th, 2012. Those servers did not have any issues with the latest updates and they are not experiencing the same behavior as the newly built servers.
I ended up comparing the IE9 Version on the cleanly install OS (No updates were installed except IE9) and the servers I built last week which were patched. The versions are exactly the same.
My findings above lead me to believe that there is a problem with the latest IE9 install package (which includes the latest cumulative update) and the Windows Update detection component.
I guess I am looking for someone to report this up the chain to get this fixed so no one else runs into this problem. I know in some cases we may not be able to see additional IE9 updates until this is resolved.

The Best Answer

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I just started having the same problem.
I was creating a new VM in Vsphere from our 2008 R2 SP1 image and it hasn't been updated and repacked in a while, so i have to install about 60 updates, including IE9.
I went through my normal setup as i had just created 2 VMs and updated them on Monday with no problem.
I got the same error code as you. The install looks like it installed IE9, but the update is still showing up as available in Windows Update.
I deleted the VM, created a new one, chose all updates except IE, then did that and it still shows up again.
Then i deleted the VM, installed just IE 9 and it still shows up as available on reboot.
I have a script that i can use to reset/clear WSUS cache on the computer, (Software distribution folder, and the windows update log, and recreates a certificate), so i tried that and then rebooted and it still showed up.
I then decide ok, maybe the Image got messed up somehow, so i started creating a new 2008 R2 install from scratch last night and chose to update just IE9 as the first install. I did that, rebooted and it didn't show up in Windows Updates, so i though GREAT.
I proceed to kick off the 100+ downloads needed before i left and left the console up.
When i got in to work this morning, the updater seemed stuck on 31 of 102 updates, this one in particular: KB288516. I rebooted the computer, because it wouldn't stop and just seemed stuck since last night, which these updates should only have taken about
an hour to install at most. I log back in and sure enough, it now shows Internet Explorer 9 at the bottom of the update list as being needed for install.
I believe this is Patch Tuesday week, so maybe they screwed up something with the Windows Update detection engine, because it worked fine on Monday when i had to update IE9 on 2 VMs that i created.