Windows keeps corrupting WU stores

I'm not sure if somebody else had this problem before, but for me this keeps happening every couple of weeks. It happened for the third time recently.
Out of the blue on shutdown Windows says that it's installing updates with the typical counter of percent complete going up. This is weird for a couple of reasons. First, no new updates were available. Second, the updates are configured to be confirmed, so
they cannot be applied automatically. I have confirmed in the update history that indeed no update was installed at that time.
So, on the next startup Windows finishes installing fictional updates again with the typical counter going up until it reaches 100% and then the message is displayed that Windows Update Cleanup is taking place (or something to that tune - I don't remember the
exact message). This step takes considerable time, I'd say at least 15 minutes with heavy disk I/O. Then when I'm finally able to login the CPU spikes with TrustedInstaller hogging one CPU core. When TrustedInstaller finally is done with its thing (a long
time, 2 hours or so) I get a pop up balloon saying that new updates are available. The problem is the "new" updates are quite old and I'm positive that they were installed before. Previously it was .NET framework fixpak or something like that, and
this time they are some security updates, one of them even dating back to 2012. If I let the updates to be applied the same set of updates will be displayed again and again. There is no way of getting out of this vicious cycle.
Obviously, Windows Update stores keep getting corrupt, but my question is why Windows keeps doing this to itself?
The Windows application error log has lots of informational events 1001 WindowsWcpOtherFailure3 pointing to Windows::Rtl::SystemImplementation:: DirectRegistryProvider::SysOpenKey API call (I assume). There are more details in those events, but I don't think
those details are very relevant here.
Is there a way to restore just the WU stores from backup? What I've been doing so far was to restore the whole partition from the latest image (taken monthly) and then restore all the user data from backups, but this is extremely tedious and time consuming
process, and it seems to be only a temporary fix, as like I said this keeps happening every couple of weeks and there is no reason to believe that it won't happen again.
I'd appreciate all the suggestions as to why is this happening and how to fix the issue without resorting to complete partition restore and then restoring the user data.

Hi Andy,
Thanks for suggestions. I've already the latest update agent installed on my system. I've reset the WU components, but that didn't help. I'm getting error 80070002 (most of the time) and occasionally errors 80080005 and 80244010. When I checked the WindowsUpdateClient
log that you pointed me to I noticed the same error 80070002 first appearing on 1/25. That's about the time the corruption happened. Before that date there were only informational entries, no errors.
I ran System Update Readiness Tool and this is the log file:
Checking System Update Readiness.
Binary Version 6.1.7601.22471
Package Version 22.0
2014-02-01 14:23
Checking Windows Servicing Packages
Checking Package Manifests and Catalogs
Checking Package Watchlist
(f)    CBS Watchlist Package Missing    0x80070002    Microsoft-Windows-Foundation-Package~31bf3856ad364e35~amd64~~0.0.0.0    Package_2_for_KB980232~31bf3856ad364e35~amd64~~6.1.1.0    Package
registry presence failed, possibly an orphaned package on package watchlist
(f)    CBS Watchlist Package Missing    0x80070002    Microsoft-Windows-ServerCore-Package~31bf3856ad364e35~amd64~~0.0.0.0    Package_2_for_KB980232~31bf3856ad364e35~amd64~~6.1.1.0    Package
registry presence failed, possibly an orphaned package on package watchlist
Checking Component Watchlist
(f)    CBS Watchlist Component Missing    0x80070002    amd64_microsoft-windows-smb10-minirdr_31bf3856ad364e35_0.0.0.0_none_089d1cba4bf65af1    Package_2_for_KB980232~31bf3856ad364e35~amd64~~6.1.1.0  
 Package registry presence failed, possibly an orphaned package on package watchlist
(f)    CBS Watchlist Component Missing    0x80070002    amd64_microsoft-windows-smb10-minirdr_31bf3856ad364e35_0.0.0.0_none_089d1cba4bf65af1    Package_2_for_KB980232~31bf3856ad364e35~amd64~~6.1.1.0  
 Package registry presence failed, possibly an orphaned package on package watchlist
(f)    CBS Watchlist Component Missing    0x80070002    amd64_microsoft-windows-smb20-minirdr_31bf3856ad364e35_0.0.0.0_none_0ad386cc8a4d8e62    Package_2_for_KB980232~31bf3856ad364e35~amd64~~6.1.1.0  
 Package registry presence failed, possibly an orphaned package on package watchlist
(f)    CBS Watchlist Component Missing    0x80070002    amd64_microsoft-windows-smb20-minirdr_31bf3856ad364e35_0.0.0.0_none_0ad386cc8a4d8e62    Package_2_for_KB980232~31bf3856ad364e35~amd64~~6.1.1.0  
 Package registry presence failed, possibly an orphaned package on package watchlist
(f)    CBS Watchlist Component Missing    0x80070002    amd64_microsoft-windows-smbminirdr_31bf3856ad364e35_0.0.0.0_none_ff89fe6651a51c8f    Package_2_for_KB980232~31bf3856ad364e35~amd64~~6.1.1.0  
 Package registry presence failed, possibly an orphaned package on package watchlist
(f)    CBS Watchlist Component Missing    0x80070002    amd64_microsoft-windows-smbminirdr_31bf3856ad364e35_0.0.0.0_none_ff89fe6651a51c8f    Package_2_for_KB980232~31bf3856ad364e35~amd64~~6.1.1.0  
 Package registry presence failed, possibly an orphaned package on package watchlist
Checking Packages
Checking Component Store
Summary:
Seconds executed: 2877
 Found 8 errors
  CBS Watchlist Package Missing Total count: 2
  CBS Watchlist Component Missing Total count: 6
I also found DeepClean.log, which is I believe what Windows did to itself to break WU. It's way too big to paste the content here.
I believe that error 80070002 has nothing to do with temporary update files, because deleting them (part of the WU component reset) doesn't help. I did this several times. I need to somehow restore the missing packages/components listed in the log file.
Where are they normally stored?
Thanks.

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