This is a bug with the SCOM 2016 agent and a bit of an annoyance when deploying update rollups as it's handy to know which agents need to be upgraded and which ones don't.
A quick check in the Agent Managed view of the Administration workspace will show a version for the agent but this version won't update to any new UR versions. The following image shows the default SCOM 2016 agent version even though I've deployed UR1 to this environment months ago...
Now, if you're thinking that after an update, all agents always drop into the Pending Management view of the Administration workspace and patiently wait until you're ready to upgrade them, then you'd be wrong. Unfortunately, depending on how you deploy the update rollup (e.g. non-admin permissions, manually installed etc.), there's a good chance that some if not all of these agents will not appear in Pending Management and you'll end up with something similar to this...
So, now your only option in the console to upgrade the agents is to run a series of bulk Repair jobs from the Agent Managed view on all of them and then hope for the best that all agents have been successfully upgraded. This is not a fun process and I really don't like having a central view of all my agent versions direct in the console.
Thankfully Microsoft's Kevin Holman (SCOM Deity and all-round awesome community contributor) has created the new SCOM Agent Version Addendum Management Pack to help address this exact problem!
This management pack runs a script that disables the built in discovery for Microsoft.SystemCenter.DiscoverHealthServiceProperties (which has a display name of 'Discover Health Service Properties') and replaces it with a new discovery that attempts to retrieve the actual update rollup Agent Version value from a DLL file in the agent installation path.
Straight after I import this new MP, my agent version in the Agent Managed view changes to reflect the existing agent versions (the 8.0.10931.0 version shows the UR1 agents that I currently have running) and after I've deployed UR2, I can select those agents for a Repair job as shown in the image below...
When the Repair job has completed, the version changes to show that my agents have now been updated to UR2 as shown here:
I love this MP as it adds some much needed functionality to the Agent Managed view within the console. An extra bonus is that this MP also works perfectly on SCOM 2012 R2 too!
If you want to know more, check out Kevin Holman's blog post here and you can download it directly from the TechNet Gallery here.