I’ve noticed recently that after I’ve updated my SCOM 2012 R2 Management Servers to UR2 my SCOM (MMA) agents are not updated. Even though my agents were listed in Pending Management for update and I’ve executed update on all of them trough the console none of them received UR2. You can check if your agents have UR2 installed in Monitoring pane –> Operations Manager –> Agent Details –> Agents by Version view. In Patch list column you should see “System Center 2012 Operations Manager UR2 Update Patch;” for those agents who have the update. Keep in mind that for SCOM (MMA) agent there was not UR1 so Patch list will either be empty or will contain “System Center 2012 Operations Manager UR2 Update Patch;”. Unfortunately I couldn’t find any resolution on how to update your agents trough the console so the only workarounds are to do it manually, trough SCCM or with Script. The agent version is not changed you will only see SCOM 2012 R2 Agent UR2 listed in Programs and Features –> Installed Updates. After you update them you will see Patch list column being populated in minute like this:
Tip from Jono Lewis: If you repair the agent it will be repaired with UR2.
Cloud Administrator in Azure World 
So they have been missing something in the update rollup package which is covered when running a repair. And we have seen problems with the updates version not displaying correctly before.