I've come across the same issue and was sure it was a ConfigMgr \ Client Agent \ WUAgent \ WMI etc. issue. But, I found the following
https://support.microsoft.com/en-us/kb/2919355
All security and non-security updates will depend on the April 2014 roll-up noted above... If you install manually, you will need to install the package in a specific order noted below.
1) clearcompressionflag.exe 2) KB2919355 3) KB2932046 4) KB2959977 5) KB2937592 6) KB2938439 7) KB2934018
Prior to me installing KB2919355 if I would only see 48 Instances when querying WMI (SELECT * FROM CCM_UpdateStatus) which is in the following WMI Class (Root\ccm\SoftwareUpdates\UpdatesStore). After installing them and forcing a Scan \ Deployment evaluation cycle and resyncing compliance state messages I now see 421 instances. I can correlate these in the UpdatesStore.log and they show up as "Missing" Updates which correlates to my Compliance Reports.
Not a bad idea to update WUA on the server. The following URL will point you to the March 2016 update. You will not be able to install this until KB2919355 is installed...
https://support.microsoft.com/en-us/kb/3138615
Hope this helps...