I am having the same issue but just recently. SCCM 2012 sp1, running on Server 2008 R2, WSUS version 3.0 SP2 3.2.7600.226. I have 3 updates with download errors of the Microsoft Software License Terms, all others are good. I have done the suggested fix un-selected SUP classifications, ran wsusutil reset, manual sync, which did timeout, selected SUP classifications, ran manual sync and still same results. So with the failed sync my SUP is syncing every hour instead of on the configured schedule. My SCCM server has been up since Oct. 2012,
Prior to running wsusutil reset Event viewer error
Source - SMS Server
WSUS Synchronization failed. Message: WSUS server not configured. Please refer to WCM.log for configuration error details..Source: CWSyncMgr::DoSync.The operating system reported error 2147500037: Unspecified error
After the reset Event viewer error
Source - SMS server
WSUS Synchronization failed.
Message: Failed to sync some of the updates.
Source: Microsoft.SystemsManagementServer.SoftwareUpdatesManagement.WsusSyncAction.WSyncAction.SyncUpdates.
The operating system reported error 2148734208:
Source - Windows Server Update Services
Content file download failed. Reason: HTTP status 401: The requested resource requires user authentication.
Source File: /msdownload/update/v5/eula.......
So progress but not resolved. A side note, I had been off for a few weeks and upon returning I found that the C drive was almost full, I found over 19 GB of logs in C:\inetpub\logs\LogFiles\W3SVC1 & W3SVC388031976. I deleted all older than 6 months. So WSUS services had all sorts of errors along with other services in the event viewer about the low disk space. The server has 2 drives, the WSUS content folders reside on a second drive which has over 20 GB of free space.
I have read about some issues with Server 2012 requiring a patch of WSUS to fix a similar issue, could there be a patch for 2008 R2 as well?