We went through a major issue with PC's not showing up. Ours turned out to be caused by the disk duplication process. These SID's are not deleted by sysprep.
On the PC in question, navigate to HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\WindowsUpdate\
You will find two keys there
"AccountDomainSid"
"SusClientId"
Back them up and then delete both.
Also check
HKEY_LOCAL_MACHINE\SOFTWARE\Policies\Microsoft\Windows\WindowsUpdate\
The "WUServer" should be pointing to your WSUS server.
Then from the command line type,
%SystemRoot%\system32\wuauclt.exe /resetauthorization /detectnow
Wait a few minutes and reboot. It should show up in WSUS then.
We had a major issue when we first started using WSUS. We have 2,100 PC's but only 1,600 were showing up. I had to create a script to check the WSUS SID on every workstation. That's when I found that we had about a dozen SID's being used repeatedly. After I knew which SID's were being reused, I created a login script that compared the workstation WSUS SID to a .txt file that contained a list of duplicate SID's. If the workstations WSUS SID was on the list, then a script ran that removed the duplicate and then it had the workstation request a new SID from WSUS.
Hope this helped,
Roger