What I found is trying to update my agents from CU2 to CU4 resulted in a common result, the agent would look like it had updated ok but when you check the SCOM agent for the agent version, it would still report CU2.
There is some information regarding updating of agents from CU3 to CU4 failing and a reboot and repair of the installation would fix this false reporting in the SCOM console. I did not find this fixed my issue when all my agents are on CU2. To fix the issue the only resolution I found was as follows;
– uninstall the existing scom agent
– install the scom agent from the scom server agent directory (this installs the scom agent with no CU)
– reboot the server
– apply CU4
I have tried a number of combinations before resorting to uninstalling the agent but none of them resulted in a fix.