I ran a patching job using a catalog with all of the relevant Microsoft filters set from a test 8.2sp4 application server. I have selected the 'group' option including Security Patches and excluding Service packs in the patch analysis job. I ran this job against a newly built Windows 2012 Server and then ran the Microsoft Baseline Security Analyzer against the server and it showed no missing patches except those relating to .Net 3.5 where it was missing all of the patches relevant for .Net 3.5 :
I have checked KB2729462 in the catalog and it shows 'Windows8-RT-2012-KB2729462-x64.msu-MS12-074-en-WINDOWS SERVER 2012 STANDARD (X64)-GOLD' so the hotfixes do appear to be there. I cannot find the trace.txt file as it doesn't seem to be used by the 8.2sp4 agent.
We have the '.Net role' enabled which installs .Net 3.5 and .Net 4.0 in addition to the default .Net 4.5 on Windows Server 2012. Only the .Net 3.5 patches appear to be missing.
User Error. .Net install job silently failed the first time and was run afterwards.