I encountered the same problem. The issue is known to Microsoft. They advise:-
Known issues with this security update
- After you perform a clean installation of Windows 7 or Windows Server 2008 R2, and then you upgrade from Internet Explorer 8 to Internet Explorer 11, you may receive an error message that resembles the following:
Windows Update encountered an unknown error
error code 80092004
After the clean installation, Windows Update continues to offer KB3038314 even though the security update may already be correctly installed.
If you receive this error message, click About Internet Explorer on the Help menu to determine whether the security update was installed. If the Update Versions line shows KB3038314, this indicates that the security update is correctly installed and that the system is not in an unprotected state.
Microsoft is researching this problem and will post more information in this article when the information becomes available.