Newly converted Windows server 2012 isn't updating

Question

Just last week I took a Windows Server 2008 VM server and did an in-place upgrade to Windows Server 2012 R2. The upgrade seemed to go off without a hitch. Now that it's properly showing as a 2012 server though, I can't get it to update. I have an enclave environment with our own WSUS server, and the WSUS server shows it now in the correct 2012 server group and shows it checking in. It shows that this server has 213 updates waiting for it (no surprise). However, when I run Windows Update on the newly converter server it always returns "no updates".

I checked the CBS.log file on the offending server and it seems to have entries for a bunch of updates, but says things like "No Parent found, go absent". Checking for the term 'fail', I also see messages like:
"Failed to start upload with file pattern: c:\windows\servicing\sqm*_std.sqm, flags: 0x2 [HRESULTS = 0x9000400 - E_FAIL ]"
"Failed to start standard sample upload"
"Failed to upload all unsent reports"
"Failed to internally open package [HRESULT = 0x800f0805 - CBS_E_INVALID_PACKAGE]"
"Failed to OpenPackage using worker session"

I can't tell if any of these kinds of messages are true 'failure' messages or not, but I find it odd that when I run Windows Update it doesn't come back and say that it Failed, it just comes back and says there aren't any updates... which is clearly not the case?

Answer 1

In-place upgrades are never recommended for a number of reasons.

If your installation media was a gold or RTM version then you'll need to install this set as a prerequisite. When 2012 R2 RTM'd the updates were called rollups and were not cumulative and they also had to be installed sequentially in correct order.
https://www.microsoft.com/en-us/download/details.aspx?id=42153
https://www.microsoft.com/en-us/download/details.aspx?id=42334

then at this point; or if you installed Windows Server 2012 R2 with Update then you can start using the cumulative updates here.
the latest SSU
https://www.catalog.update.microsoft.com/Search.aspx?q=KB4566425

followed by the latest Monthly Rollup
The latest always contains new fixes plus the previous monthly update.
https://support.microsoft.com/en-us/help/4009470/windows-8-1-windows-server-2012-r2-update-history

--please don't forget to Accept as answer if the reply is helpful--

Answer 2

Regardless of the actual cause of the issue, I was able to get it working again by executing the following commands on the server from an elevated command prompt:
sc config wuauserv start= disabled
sc stop wuauserv
ren %windir%\softwaredistribution softwaredistribution.old
sc config wuauserv start= auto
sc start wuauserv

After this, I rebooted and then it finally showed that it correctly had over 200 updates (2012 updates) to work through. Issue resolved!